I know about BIOSes and selecting the boot drive, I have plenty of PCs (both virtual and physical).

What I'm not sure on is whether when you do that to a Window machine whether all your other drives appear on the drive letters you (and your software) expects ? Modern partitioning schemes have unique ids for drives/partitions to allow stuff like this to work ok in theory, but I don't know how Windows handles it (and if it does, whether it requires you to have used the newer partitioning schemes).

Definitely at some point in the past it didn't handle it well, I remember drives shifting letters when things went wrong in machines with a few drives/partitions.