You need to do 2 things; fix boot.ini and then delete the unwanted stuff
wherever it is. It may be an artifact of a failed install. Not
absolutely necessary to delete it, but it'll save space if you do.
1. On the system drive, note carefully the contents of the file
boot.ini. (It's a small text file with the hidden & system attributes
set, so to display & then edit it you must remove those attributes.
Print it out or save a copy as boot.inj before diddling with it.)
In that file you'll see what's displayed at boot time. Both the boot
options you have are appear in it; make sure you know which is which.
Then delete the whole line pointing to that useless boot directory, and
save the edited boot.ini file as boot.ini.
Then boot the machine to make sure you only get the option you want. At
this point you shouldn't see any boot options menu at all; the system
should simply go immediately to your working W2k & load it.
2. When you've checked that all is well, you can delete in its entirety
whatever directory (and its subdirectories) the unwanted entry was
pointing to.