Not sure that this is the 'cleanest' way of doing it, but
here is a suggestion.
I assume you are 100% sure you will not be starting
Windows 98 again. Also, I assume that Windows 98 is
installed to a different directory to what Windows 2000
is. In which case, you can simply remove the windows
folder that contain Windows 98. However... make sure
you do not have any strange applications on Windows 2000,
that might have been written to reference files found in
C:\Windows (rather than %systemroot%), otherwise you
could be about to blow away some application dlls for
example. If your apps are standard off the shelf stuff,
then you should be ok.
After that, edit the c:\boot.ini file. The boot.ini file
contains the list of operating systems that form the boot
menu at startup. I assume you start Windows 98 using an
option on an Operating System selection screen?
CAREFUL!!! Get the boot.ini wrong...and you face another
problem to sort out!! You should only need to remove a
single line I would think.
Hope it helps. As I said, it might not be the cleanest
way of removing it, and somebody else might have another
idea, but this is the way I would go.
