With a dual boot win2k and win me you can simply delete every win me file on the partition or drive .
Then change the boot ini and delete de windows me line .
As win2k is nt 5 and if they use the same ntldr and ntdetect.com there should be no problem neither , at least I suppose. Ther will be a way to repair your boot system too , with the winnt cd if something goes wrong
To know others is wisdom !
To know yourself is enlightenment !