Alright chaps. Another one for the technophiles out there

My girlfriends computer (running Vista) recently stopped booting up. After trying everything I knew, including system restore, I re-installed vista.
Now, she has two hard-drives. One very full, and one hardly full at all. The latter is where I thought windows was installed, but it wasn't.
So now I there are two hard drives, each with Vista installed. One works, the other doesn't. When the computer boots up it asks which version to boot with. [Isn't that basically Dual/multi-booting... even if its two of the same OS?]
But I guess what my question is, can I delete the bad OS completley and there not be any side effects? I've always been deeply suspicious of meddling with anything in the Windows folder, and I am reluctant to touch it, even if it doesn't work, for fear of buggering the whole thing up entirely.
Any suggestions?