Sounds like chkdsk might have run & found some errors.
Boot into XP & from there access the 2000 partition/HD, now look for a folder called "found.000" in the root directory C:\ if 2000 is installed on C: drive.
If there is a "found.000" folder you'll need to open it & see what's inside, I had chkdsk recently rename & move my system32 folder to the root directory all files completely intact inside. Since I was dual booting all I had to do was rename the folder & move it back to the WINNT directory & the problem was solved.
If it's not a chkdsk issue & you can still access the 2000 partition/HD, check the boot.ini file & make sure 2000 is still listed as a boot item.
If you post the exact error it'll be more helpfull.