Install Linux on your partition & ask for lilo/grub to be installed in the boot record of that partition alone & also make sure you do a boot floppy.
Boot on that floppy & do Phantasm's patented spell of multi-boot ghost summoning. In case you're not familiar with it, type this ->
dd if=/dev/<partition-onwhich-you've-installed-linux> of=/bootsect.lin bs=512 count=1
Copy that bootsect.lin file on a floppy or on a FAT partition ( Linux won't write on an NTFS partition ). Then boot windows & modify the boot.ini file by adding Part 2 of Phant's patented spell of multi-boot ghost summoning like this ->
c:\bootsect.lin="My Cool Linux"
Now whenever you need to re-install Windows, back up the bootsect.lin file & once you're done re-installing windows, recopy the file where the windows OS loader can access it & add the line to the boot.ini file again.
That should work.