i wonder why this happened to u from the beginning!
cuase i had this case exactly, with small differences ..
i had winxp .. and redhat 7.2 ..with lilo
i formated the winxp drive and installed win2k ...
but nothing happened to the lilo!!
it was still there .!! didn't disappear .. i asked someone about this thing.. and he said that win2k boots from boot.ini and doesn't do any thing to the MBR
now i upgraded to redhat 7.3 with grub .. it looks better that hte lilo