I have a two hard-drive setup, let's say X and Y, X older than the other. My Windows installation was on X. After noticing the X hard drive started failing I decided to backup everything on Y and reinstall the system on it.
After backing everything up I deleted the system partitions on drive X, leaving around 64 gigs of unallocated space and installed Windows on drive Y.
Upon removing the failing hard drive from the system, Windows refused to boot. Upon further inspection I realized that Windows installed itself on drive Y, but it also made the 100MB partition the old, failing drive.
How can I get a working system with everything on drive Y after removing drive X without reinstalling Windows?