Forum Spotlight: How to successfully clone and upgrade a WHS system drive

by Alex Kuretz on January 17, 2010 · 46 comments

in Forum Spotlight

Forum member “ymboc” has long been a great technical contributor in the forums. First he uncovered the layout of the MediaSmart Server debug port, then figured out how to modify the BIOS of the EX470 and EX475 to use an AMD X2 processor, next he documented the registry keys that manage the fan speed of the EX470 and EX475 MediaSmart Servers (subsequently used by the MSS Fan Control Add-In), and has continued to support all the hardware tweaking enthusiasts in the forums.

Now he’s at it again with a new guide describing how to successfully clone and upgrade your Windows Home Server system drive using the uniqueid feature of the Windows diskpart command. I’ll preface this by saying this is not a solution to back up the WHS System drive, this process is only useful as a mechanism to replace or upgrade the system drive in your Windows Home Server. It is also a fairly lengthy process that requires a significant attention to detail in order to be successful, and of course this carries the risk of possibly damaging your Windows Home Server installation or could even result in data loss.

With all the scary caveats and disclaimers out of the way, here’s a description of the issue from ymboc’s forum post.

WHS uses (GU)ID numbers stored in the partition table of each disk to help identify them. When using disk imaging software to migrate an operating system from one disk to another disk, these disk ID numbers are typically not cloned during the disk imaging operation.

To Function properly, WHS requires that the disk ID number of the newly imaged disk match that of the image source.

A cloned WHS system disk with a mismatched disk ID number will still boot normally but will exhibit a number of Critical Health Warnings the most common of which is the “Backup Service is not Running” warning.

ymboc found that he could manipulate the disk ID using the uniqueid feature of the diskpart command to transfer the old Disk ID from the original disk and apply it to the new disk, allowing Windows Home Server to boot successfully with none of the warnings usually encountered. He tried this process first on a test system and then on his main home system and both worked successfully. Note that the original version of Vista does not support the uniqueid feature, you’ll need at least SP1.

I wanted to verify his findings and become familiar with the process, so I took my recently retired but still running EX475 with 3 drives in the storage pool including the stock 500GB System drive. I started by shutting down the Home Server, removing the System Drive, and inserting both it and a spare 750GB drive into my iStoragePro eSATA storage enclosure that was connected to my Vista SP2 PC. A multi-drive eSATA or USB external enclosure is the most simple way to directly attach the drives for cloning, however other alternatives are certainly possible such as installing the drives internal to your PC or by creating an image of the original disk and then applying it to the upgrade disk.

The next step was to use the “Clone Drive” feature of Acronis True Image Home 2010 to clone the original 500GB system drive to the spare 750GB drive. I selected the “Automatically resize partitions” option in Acronis so that the D: partition would fill up the new disk. Other disk imaging software or older versions may not support the “Automatically resize partitions” option, in which case ymboc includes instructions on how to do this manually. The disk clone took a bit over an hour to complete. I ended up with a 30GB system partition instead of the default 20GB system partition, with the remainder of the space utilized by the expanded D: DATA partition. This was due to the “proportional” default behavior of Acronis which resized each partition.

I wanted to verify the negative behavior of adding a cloned drive to the system to demonstrate the failure seen when the DISK ID’s don’t match, so I inserted the 750GB cloned drive into the server and powered it on. As you can see, Windows Home Server is not happy at all and my system is effectively unusable. The most common symptoms are the original System Drive showing up as missing from the storage pool, the new System Drive appearing to be Not Added, and the scrolling “Calculating sizes…” message where the usage pie charts normally reside.

I then shut down the server, removed the 750GB drive, and added it back to the eSATA storage enclosure. I followed ymboc’s instructions to read the old uniqueid from the original System Drive, and then applied it to the new System Drive. One important note: I found that I could not set the original Disk ID to the new disk, this was due to the original drive still being in my eSATA enclosure. Apparently diskpart won’t assign the same Disk ID to two drives in the system, or else it won’t display the same ID for two drives, I’m not certain which is true. Once I removed the original system drive from the eSATA enclosure I was able to successfully apply the Disk ID to the new drive.

After this completed I was ready to put the newly modified 750GB drive into the server and power it on. I have to admit to some apprehension as the system booted, and unfortunately that apprehension was justified as the system was still in a bad state similar to before I modified the uniqueid. ymboc and I discussed this, I cloned the original drive again while this time leaving the stock 20GB partition and following his resize instructions but still was unsuccessful. ymboc did some additional testing and discovered that prior to the Windows Home Server Power Packs the uniqueid was the only step needed, but with the latest Power Pack 3 this process failed.

Discouraged but not deterred, we both spent the next few days investigating and experimenting in similar directions, focused on how Windows Home Server stores data about the server drives and volumes in the Windows Registry. We identified some Volume and Disk info that was incorrect in the Storage Manager section of the Registry, and eventually ymboc made the final connection with the MountedDevices that links the C: and D: devices to their correct Volume paths. After he shared his updated process I followed it and had a successfully working system.

I’ve not run the system extensively, however I’m reasonably confident that everything is working just fine and that this is a reliable way to replace the System Drive in your Windows Home Server. While the process isn’t the full System Drive Backup that many people would like to see, it is a process that will be very handy for anyone looking to upgrade their smaller stock System Drive to a larger disk, or if you have a failing System Drive that is still working well enough to make a clone. I will remind you that this is not a process for the faint of heart, and requires a very careful attention to detail in order to be successful.

ymboc is looking for feedback from others following the process, so be sure to share your experience in his forum post or here in the comments and let us know how it goes.

Article by

I'm Alex Kuretz, and I'm the founder of I was the Lead Test and Integration Engineer at HP for the MediaSmart Server until April 2008 when I moved on to other opportunities outside HP. I've kept active in the Windows Home Server community, creating several add-ins and helping users make the most of their Home Servers.


Comp1962 January 17, 2010 at 1:28 am

Great write up! I printed ymboc’s instructions and when I purchase more drives I will perform the experiment. I do have a 1 TB Drive I use for dumping ripped DVD’s. I could pull that drive and try the proceedure and swap out the orginal 500gb drive from the server I do all my testing with and see how it flies. Then I can do the same for my primary server when I purchase more hard drives. It will be a good test to do after I complete my 2009 Taxes tomorow.

Cougar January 17, 2010 at 10:49 am

Great work guys!

Vassilis January 18, 2010 at 6:42 am

i’m sorry but i don’t get how this is not also a “not a solution to back up the WHS System drive”.
I mean you clone the system drive to a new one, how this not a backup ?

Alex Kuretz January 18, 2010 at 8:47 am

A backup implies the storage of an image for later restore, this article and guide is about taking a snapshot and instantly applying it to another drive.

The process may actually may work successfully as an OS backup of the C: partition, though my concern would be around keeping that image updated to handle patches to WHS (primarily around the Backup DB as that seems most susceptible to change), added or removed drives, and any Add-In changes. The problem would come with the state of the tombstones on the D: partition and how the are linked to the data on the storage drives. To the best of my knowledge, WHS won’t do a rebuild of the tombstones unless the system is put into Server Recovery mode. Now, we could experiment to see if we can force a rebuild of the tombstones, but at that point we’re getting way out into unknown territory.

The point being that while you could possibly/probably backup the OS image for later restore, this would only protect you from OS corruption and not from the failure of your System Disk which is why I advocate against considering this to be a full backup process.

I’m thinking out loud on most of that, as of course I’ve not tried it yet. I’m definitely open to other thoughts on the matter!

Comp1962 January 18, 2010 at 9:34 am


I still have to get to testing the process out and I have full confidence that it will work as described. The value I see in this is for those wanting to simply replace their existing System Drive with a new drive of same or larger capacity.

As far as using the imaged drive as a consideration for backup should your system drive fail and is in need to replaced I think to accomplish this you would need a dedicated drive not managed by WHS to record and monitor changes to both the tombstones and changes to the data structure on the system drive. If such monitoring software one day should exist I would imagine there would be some sort of an UPDATE function to read the data off the drive monitoring the system and then simply update the changes to the system drive to bring it upto date. To me this is the simplest way to use the imaged drive as a backup solution rather then the WHS Recovery Solution.

I am just thinking outloud here and may be out of place in my thought process but I do not think I am to far off but such software would have to be developed.

For now I am just excited and looking forward to testing this image proceedure out so that I can increase the size of my system drive without performing the WHS Recovery which as you know requires resetting up the server. This to me seems more favorable of a solution.

DVDBob January 18, 2010 at 10:16 am

Very intriguing, an something I could’ve used about 6 months ago. Oh well. Will definitely add to Delicious so I have it for the future.

As for using it as a backup solution, couldn’t one make normal backups of their System drive to whatever media they choose and if (or when) the drive fails, restore the most recent backup and do the uniqueid process? Depending on how frequently you backup the System drive, you might not be that far off from current state.

Alex Kuretz January 18, 2010 at 10:19 am

As for using it as a backup solution, couldn’t one make normal backups of their System drive to whatever media they choose and if (or when) the drive fails, restore the most recent backup and do the uniqueid process? Depending on how frequently you backup the System drive, you might not be that far off from current state.

As I mentioned above, this will likely work for the C: System partition but not for the D: data partition that contains the tombstones.

Alexander Zinchenko January 19, 2010 at 11:51 am

I used Clonezilla LiveCD when cloned WHS system drive. Clonezilla may copy disk ID too. Since September I have no any issue with WHS; BackUp, Folder Duplication and so on work fine.

Probably cloning using Clonezilla would be easier than according with instruction above.

ymboc January 19, 2010 at 2:57 pm

Alexander: Should CloneZilla infact actually clone the DiskID, that would certainly be sufficient enough to clone Pre-PowerPack1 WHS systems…

Can you pass on the details of your CloneZilla experience in the forum thread? or alternatively via forum PM?


Comp1962 January 19, 2010 at 7:09 pm

Alexander, When you cloned your system drive did you have other drives in your server or was it the only drive in use?

Alexander Zinchenko January 20, 2010 at 7:39 am

ymboc: My WHS is turned off right now because of I am out of home right now. Since my leave PP3 were released. Let me find out how my system would work with PP3 and then I will try to remember how I cloned system drive.

Comp1962: It was 3 drives in my WHS. I changed defective drive to new and colder with the same size.

David January 21, 2010 at 1:56 pm

Tranquil are soon to release a neat Safe Server – based on a Safe Server module….

Keep your eyes on for further information

We hope that now users (SQA) can have 100% peace of mind (much needed)

Nigel January 22, 2010 at 6:49 am

Sounds great. Are you willing to supply us with a review unit?

ymboc January 22, 2010 at 7:21 am

Nigel: I think tranquil’s new product is just an implementation of IcyDock’s New MB992 2-bay raid Sata 2.5 to 3.5 adapter (or a variation thereof) annouced at CES

Nigel January 22, 2010 at 10:42 am

Cheers. More than happy for icydock to supply us some review units for the site as well!

David January 22, 2010 at 11:15 am

Indeed the SSM is a custom version of a HDD caddy designed to fit the SQA-5H Home Servers. It’s not the MB992, but something a little similar. The device will drop into the SQA-5H HDD (screwless) carriers. The RAID1 function ensures HDD protection, and does not affect HDD data transfers – as detailed in a recent post on the blog.

There is no reason why any home built server could not be made this way, and we would recommend it, as long as the builder understands the hardware and software functions. We do not expect OEMs to follow Tranquil, as the hardware increase would hike the build costs up too much.

Let’s hope this signals the beginning of the end of the WHS HDD1 problems (re-building can be very tiresome)

Ethan Kayes March 2, 2010 at 11:20 am

I want to say thank you to Alex and Ymboc for this How to Guide. I just replaced my failing system drive on my DYI Home Server. And after a few minor problems I have everything working just like new!

The process as outline by Ymboc went very smoothly. I have two minor suggestions in the process. If the disk in your workstation is identical to the disk you are going to be installing on the WHS I would write down the Disk ID of your workstation prior to starting the upgrade process. So my step one would be to use Diskpart to identify the Disk ID of your workstation prior to installing the WHS system drive and the new drive for copying. (Yes I changed the ID of the wrong drive)

Suggestion number two, if possible screen print the regedit parts of your current WHS system and highlight the items that you will be changing prior to making those changes in part 3 of the guide.

Again a big thank you, you saved my WHS!


Alex Kuretz March 2, 2010 at 11:31 am

It’s great to hear this process worked for you, thanks for the feedback. Those are both good suggestions and can be useful references during the upgrade process.

Tony Dann April 26, 2010 at 7:33 am

Thanks guys for this great guide, worked fine for me as my system drive was giving SMART errors and is now replaced good as new! One question though….. why would you want a larger system drive as my WHS never seems to use the free space on D: of the system drive which is now 1TB. It uses other drives in the pool normally but the d: section of my system drive never gets used or very little use anyways.

Thanks again


Alex Kuretz April 26, 2010 at 9:28 am

Hi Tony, I’m glad the guide worked well for you. You are correct that Windows Home Server will not store data on the system drive until all other drives are close to being full. There are still a number of reasons you might want to clone your system drive, and it’s often less economical or difficult to find the older smaller capacity drives if you need to replace a failing system drive. Others are using much of their capacity and need the extra storage space of the system drive. Or you could migrate to a newer MediaSmart Server by using Server Recovery and want to use the new larger system drive that came with your EX495 rather than the 2 year old 500GB system drive that was in the original EX475 (this was my experience).

Tony Dann April 26, 2010 at 4:16 pm

Thanks for that Alex, wasn’t too sure if this was normal behavior for the system drive but glad to hear it is. I used a 1TB drive because as you say the small drives don’t make much sense $ wise.



ccp619 May 22, 2010 at 6:31 pm

Excellent post/procedure. I used it all the way through to replace my system drive in my EX470. I purposefully chose the same size drive to minimize the complexity as the cost savings was not all that high for a 1TB drive (only $20). The original drive was a Seagate ST3500630AS and the replacement drive was the same Seagate ST3500641AS-RK that I used to expand the system size last year. The system drive was not completely failed, but I could hear it was getting very loud and when I removed it two days ago, it was VERY hot to the touch. (I had received warnings that the system drive was failing.)
As for the procedure, I was able to use Clonezilla Live (as per Alexander Zinchenko’s post – thx Alex) with very little problem. I used the boot CD created by the ISO file and disconnected the drives in my WS to prevent accidental “issues” or cloning the wrong drive. I did have to use Clonezilla in VGA mode because my workstation’s advanced video card was not happy with any of the modes between 1024 and 640. I selected the advanced mode and unselected the first two options of the four it had checked by default. The first option was the one about copying the Linux boot manager and the second was about resizing. I lost only 8 GB in the process so it was not really necessary. All the UniqueID work was not necessary though I did all the steps just to verify it was correct.
Once cloned I used the steps to update the WHS registry – steps 22 and beyond. To do this, I remove the pair of extra drives in my system ( I only had to unlatch them and slide them out a half inch – prevents problems that could occur if you reinsert into the wrong slot) and inserted the system drive in its slot. I started the WHS and my workstation. After verifying the expected backup and drive errors using the normal WHS client, I was able to use MSTSC to connect to the WHS console. I updated the ManufactureName key but did NOT have to update the WHS volume info (steps 26 and 27.) After a shutdown, I reinstalled the normal drives and started the WHS normally to find there were no errors.
I really think it was a good idea to document everything carefully before starting using notepad and screen shots as it allowed me to double check everything as I went. Thanks again for the big save on this as I would not have enjoyed losing all my backups and users.

ccp619 May 22, 2010 at 6:41 pm

By the way. All the discussion about using this procedure for backups is BUNK. Backups imply that you can (like homeserver does) keep copies of your system at different times – like snapshots. It is also not a good idea to have a “backup solution” that requires dimantling your WHS and PC. Handling your drives all the time just invites disaster. It seems VERY odd to me that no one has created a procedure to stash at least the user and settings info on a second drive or off-server location. It is likewise odd that there is no way to use the system’s duplication to keep the backup data safe. I think it would be great if there was a way to dedicate a drive or use a drive attached to a pc on the network to keep the sys drive’s C and D partitions backed-up. With all the drive duplication tools out there it seems as though it would be possible even if it was a manual (vs. automatic) process. I’d take the time to backup my server weekly if it were possible.

Alex Kuretz May 23, 2010 at 8:13 am

ccp619, take a look at Windows Home Server Vail, it has I believe all those features you’re requesting here which were largely made much easier to implement by moving to the Server 2008 R2 platform.

pad March 14, 2011 at 3:48 pm

Hello, I’m thinking about buying the tranqull safe server module for my sqa5h, which uses 2 2.5in ssd in a raid for the system drive. Any idea if these instructions will work for cloning the system disk to the new? Would the raided disks be transparent and would the disk id be modified successfully?


ron May 16, 2011 at 3:30 am


I was thinking the same thing but using the icydock raid enclosure.

What happens with the DiskID? can it still be set or are there issues?



Mcougle May 22, 2011 at 3:48 pm

Just used clonezilla to tranfer the system drive off of a failing drive. worked perfect-no issues. I confirmed the diskID transfered after the process and it worked great.

Ron May 22, 2011 at 7:44 pm

Hi further to my last post. I installed two drives into the icy dock raid enclosure and did a hardware setup of raid 1 first. I then cloned the system drive and set the diskid and followed the instructions for the registry changes. All good, system runs correctly very happy with my WHSv1

AD July 29, 2011 at 6:50 am

This is exactly what I plan to do, already have a couple of the MB982SPR-2S icy dock raid enclosures (one for main WHS, one for secondary/testing WHS). My existing system disk in my EX490 main server and Tranquil secondary server are both 1TB and don’t really want the hastle/additional expense of having to buy 4x 1TB 2.5 drives to make this happen. I already have a couple of old 120gb 2.5 drives I plan to try this with and if that goes well will probably get something in the 400gb-640gb range for the main server. The drive size difference will no doubt mean I can’t use the clone option when imaging and will need to image and restore instead, of course the current ‘in use’ capacity of the system drive will need to be within the size limits of the new drives as well – other than these points can anyone see any potential issues?

Michael Lee December 14, 2011 at 10:34 am

Do you have a write-up of how you RAIDed your system drive? I am looking to do this with my HP ex495 but not sure where to start. I tried to google it with no success.

Is this safe to do and have you successfully pulled out a drive with no issues?

jonrob August 22, 2011 at 2:02 am

this worked a treat only wished I had read it 3hrs earlier after trying non successful solutions

Steve September 21, 2011 at 6:59 am


I have gotten several good years out of an HP ex485. The sys drive is requiring replacement in the near term. It is still working now.

Are WHS Server Recovery and cloning essentially equivalent options? With Recovery, do I have to reconfigure the server by adding back accounts, add-ins etc? Is one of these options relatively easier to accomplish in this situation. I have plenty of excess storage on the server and to need to resize the primary drive.

Alex Kuretz September 21, 2011 at 8:14 am

Server Recovery requires you to reconfigure the server, download all updates, re-install add-ins, and re-create users. Your data on the remaining drives should remain intact as long as it’s duplicated, however if some of your backup database resides on the system drive that you replace it is possible to lose some or all of your client backups.

Cloning the drive is exactly that, a clone of what you have now.

Steve September 26, 2011 at 5:27 pm

I don’t understand why this works but man that was easy. Thanks! I used clonezilla as described by ccp619 along with your directions. No issues and it handled resizing automatically.


peter November 18, 2011 at 3:42 am

Tried to clone a 2TB WHS v1 system drive (2TB Samsung HD204UI F4-slow drive to a Western Digital 2TB WD2002FAEX007BA0-fast) with Acronis 2012 home.This threw up a lot of errors when clone drive used in the system.
I was about to give up until i read about clonezilla and used this to clone my system drive instead of acronis. I could not believe it, the system started without any kind of errors. After doing the registry checks, the *ONLY* thing i needed to do was step 25) “Updating the Name of the System Drive as it appears in the WHS Console “Server Storage” Tab” Happy days :)

peter January 19, 2012 at 3:45 am

Just an update, the WHS v1 is working fine with the cloned system drive.
Many thanks to the people who contributed to this thread.


Mondo April 8, 2012 at 8:21 pm

Regarding Clonezilla – I’ve been using it for years to clone PCs at work. I’ve thought about using it to clone my home WHS system drive. I’ve Googled some in the past and have seen posts where people say “cloning software will cause problems with WHS” etc. So, I’ve never actually tried it. Thinking about trying it now though, after a scare with my system this weekend. Turned out to be a bad drive in the pool but it took a while to figure out. Kinda hard with a headless unit when the console won’t load!

So, some folks have used Clonezilla to clone their WHS system drive without problems? If it’s a true clone, then it copies disk id’s, right? I also have access to a diskjockey hardware drive cloning device. This could work too, right? Anyone ever try it?

Alex Kuretz April 9, 2012 at 8:50 am

The forum topic linked in the article has lots of discussion on the process including feedback on people using Clonezilla.

peter April 11, 2012 at 1:15 pm

Well i used clonezilla to image my system drive with no probs. Please follow the above link given by Aex.

Gud luck.

Ian June 24, 2012 at 4:41 am

Sorry if I been stupid, but cant actually see a link to an actual article that has these steps described for us mere mortals to follow!!!

Can someone point me in the right direction please?

Alex Kuretz June 24, 2012 at 9:33 am

It’s linked a couple times in the article, in particular in the last paragraph where you are directed to the forums. Here’s the direct link.

ChuckN September 6, 2012 at 8:29 pm

A year or so ago I used this procedure to swap my server’s system disk for a 2 TB one. I’m running 2.5. That disk was failing, so I cloned it with an Aluratek AHDDUB100 disk duplicator ($50 as a NewEgg ShellShocker). It carried the original disk’s uniqueID to the new disk; I plugged it in and it’s working fine.

No complaints from the WHS console about the disks (said all drives were healthy), but I went through the registry changes anyway, updating the ManufactureName — everything else was okay.

Thanks much for the instructions!

peter September 7, 2012 at 7:12 am

Just wondering, why pay $50 when Clonezilla can do it for free? Please see my earlier post.

Comments are closed, visit the forums to continue the discussion.

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