Unless there is a known issue with the system drive I would not bother to replace it. If your simply looking to increase your capacity its far better to just add another drive known to work well with WHSv1 into one of your open bays.
The drive issues with WHSv1 these days have to do with the newer AF or Advanced Format drives. Some need to be prepared for use with WHSv1 while others are plug an play. This has more to do with the 4K Sector Size used by AF Drives where as WHSv1 is designed to be used with drives that use 5b sector sizes.
I would also recommend you install the ADD-IN BDBB and backup your client backup database if its important to you this way if something were to go wrong during a recovery you could restore the client backup database from the BDBB Backup and it does work quite well. I have used it in the past with external drives but for me some of the client backups are for offsite clients so I need to protect those at all cost.
If you perform a Server Recovery you will not lose any data that has been duplicated but any data stored on the DATA Partition of the System Drive which has not been duplicated will be lost when you change the drive and this includes Client Backup Data.
You can as Ruben Rocha read the drives in a client which has been setup to view hidden files and folders. On the system drive these files would be located on the DATA Partition in the hidden folder named DE. All storage pool drives are named DATA and likewise the files can be found in the same DE folder.
Again if your system drive is in good condition then I would not be in any hurry to perform a Server Recovery its just not worth the headache or time it will take to fully perform a recovery. Also you will want to make sure the one storage pool drive is in good working order before you perform any recovery.
Last thing worth mentioning is if your really set on changing the system drive and if its in good condition you may want to opt to clone the drive rather then perform a recovery. Its a bit of a process and somewhat complicated but if done correctly it takes less time then a recovery and you will lose nothing that is not duplicated.
For more information on how to clone a system drive review the info in the following link:
http://www.mediasmartserver.net/2010/01 ... tem-drive/As for Advanced Format Drives kindly perform a site search on them to find out what others are using and to learn about the issues you could run into because its a bit on the complicated side.