Re-formating 1 of 2 HD’S???

Hello everyone, here is what i would like to do…….

I have 2 HD’S installed….. the first one has WIN-XP (Upgraded from ME)FAT32
The second HD has Win2kPro….NTFS

I would like to reformat(to cleanout)the first HD but still need to be able to access the 2nd HD and Win2KPro….

I THINK what will happen if I do this is the boot file for Win2K will be erased and wont be accessable after refromating and clean-installing XP on the first HD…..

What about if I copy this file to thesecond HD and load it back in after installing XP back on the first HD??
I want to reformat the first HD ASAP……
Thanks for any advise……