hi case, welcome to the forums,
i'm not sure if i've understood you correctly. are you saying you have a dual-boot vista/7 system with the os's on separate drives? and you want to reformat the 7 drive without affecting vista?
yes - that would be fine. right at the start of the 7 install you will be asked which drive/partition you want to install on. choose your current 7 drive, format, and install.