Hi,
Just edit the boot.ini file and remove reference to 2000. You could try finding your 2000 on the drive but if you have plenty of space, just leave it there.

If windows 2000 is in a different partition than windows xp pro, log into xp and go to that partition which will show in another letter. Right click it and format.

Then you have to modify the C:\boot.ini file where the entries for choosing boot are.
That's a hidden file usually. Un-hide it by:
explorer->Tools->Folder Options->ViewTab. Click Show hidden files and folders. Apply.OK.
To modify that file you need to temporarily change the attributes from read only. Right click boot.ini->properties->un-click Read-only->Apply.
After that open it in any editor and delete any entry that has windows 2000. Save and change back the attributes to read-only.