Changing the Windows drive letter is not advisable. It has a 50/50 chance of failure.
I have though, had instances where multi-boot systems would either corrupt or overwrite another OS's boot records, even after a second or third boot, so there is the remote chance that the mbr corruption is unrelated to the drive change. There are ways to recover a mbr manually, outside of Windows and without a repair disk, but I haven't done that in ages and would be lying if I said I knew how to do it at this point. You could try EASUS partition manager, if you have a running Windows at this point in time.
Btw, why are you switching boot order through BIOS? Generally Windows will pick up on any additional installations and add them to the boot select menu.