I recently wanted to format my Vista partition and use it for extra storage when I discovered that the Windows Boot Manager, responsible for starting up Windows, actually resided on the Vista partition rather than on my W7 partition. This meant that if I simply formatted the Vista partition, Windows 7 wouldn’t start and the BIOS loader would complain about a missing boot manager.
After searching through heaps of sites and not finding anything useful (with the possible exception of this forum post), it turns out that both the Windows Vista and Windows 7 installation DVDs contain a tool specifically for repairing system boot problems.
A quick deletion of the Vista partition followed by 2 (yes, 2, not 1) repairs from the Windows installation DVD essentially “moved” (actually recreated) the Windows Boot Manager on my Windows 7 partition. The first repair recovers the “lost” Windows 7 partition and requires a reboot. The second repair recreates the boot manager.
Of course, I still recommend you clone your entire disk before trying something like this. Memory is cheap, but data is priceless.