I guess that you could remove the entry in the boot.ini file that gives you the option of Windows 2000 and then you could remove the WINNT folder. I would think that would work but if not, you may have huge problems, like not being able to start Win98 at all.
You could try doing it all temporarily first. Change the boot.ini file and save a copy of the old boot.ini file and rename the WINNT folder to something like WINNTB. Then see if that works. If not, you can change them back in DOS (assuming you know your way around DOS and you have a DOS boot diskette). If that does work, in a few weeks you can delete the old boot.ini file and the WINNTB folder.