How does Windows number its disks? By numbering, I mean the physical disks, which Disk Management calls Disk 0, Disk 1, Disk 2, etc.
My C and D partition used to be on Disk 0 and my E partition was on Disk 1. Now, however, my C and D paritions are Disk 1 and E is on Disk 0.
I have a backup product which backs up based on the disk numbering, so when this changes, it messes up which disk should be backed up.