I have 2 HDs, one scsi, if you have to reinstall windows, its possible in some cases to just bounce the programs and data to the second HD (the one without windows,) and then reformat the original disk. I've actually always had to reformat the disk, the stupid windows installer never seems to work otherwise...
...Yeah, but its sooo nice usually to have a clean windows install, as it fixes (usually) all the wierd stupid errors and plus it cleans up all the superfluous icons and stuff, plus you dont have to keep looking for special tweaks to fix the original error.
Windows is evil though, very evil, and seemingly buggy when you have lots of games...