My win 10 Pro 64 bit laptop finally completed the upgrade to version 10586.29.
My EX 475 had a Network Health warning, said the laptop had a new hard drive

Windows created a 455 mb recovery partition on my primary drive.
Windows Disk management shows the entire 455 mb as free space, Windows home server backup shows 378 mb used.

I had to reconfigure the backup for the laptop, I will see if backs up tonight!

I just had a problem restoring a laptop because I unchecked the system reserved partition from the backups and had to do some voodoo to get it back.
I would say you are doing the right thing by backing up the entire disk. It will take up a bit more space, but I think it will be worth it later if you need to recover a pc.
I'm guessing it is continuing to backup ok, the first one was probably slower, but the next one should be faster as the contents of that partition most likely won't change much if at all.
Good Luck

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