This is a very common issue when willing to switch from a temporary Dual Boot (for a test/data transfer phase) to a unique OS Boot (i.e. the most recent one)
I had windows XP on and IDE HDD, "Disk 1". I then installed windodws 7 on a SATA HDD, "Disk 2".
Dual Boot worked for a while, then I started having a disk-read error while booting, and when I succeeded in booting and chose Windows 7, "Disk 1" was often marked unallocated. (probably an IDE/SATA Conflict involving AHCI)
All in all, as I do not need the XP System anymore, what I would like is to definitely get rid of "Disk1", but I assume boot info is on it. Is there a way of moving boot info from "Disk 1" to "Disk 2" or any other way to make the system boot the current Windows 7 without the need of Disk1 (Building a BCD from scratch on "Disk 2") ?