you run into the same issue as i have.
had vista on hdd1, installed w7 on hdd2, u want to keep w7 now and remove vista from hdd1/perm, but you cant format hdd1 because it has the system boot (mbr) information on hdd1.
i found some links on my thread that might come handy for you, but i haven't tried it myself yet. basically you have to move the mbr to the hdd2 w7 drive. you can see on disk management -> hdd, you will notice hdd1 is indicated as the System, so you can't format it/etc.