If you set this dual boot up the normal M$ way (ie, win98 installed first, then 2k, so you have a 2k boot menu with entries for both operating systems) you'll need to create a boot sector for the 2k drive/installation before you remove the 98 (as both will currently be using boot sector on the win98 drive).
You can do this easily enough. Copy the files ntldr, ntdetect.com and boot.ini from the root of C: (win98 drive) to the root of the 2k drive (hidden, readonly, system files, so treat accordingly to find/copy them - I'd run attrib -s -h -r C:\*.* from a command/dos prompt).
Now edit the boot.ini file you've just created on the 2k drive so it looks like this:-
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINNT
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINNT="Microsoft Windows 2000 Professional" /fastdetect
(it should currently have rdisk(1) and an entry C:\="Microsoft Windows"
Now run 2k's recovery console and the fixboot command (fixboot X: - where X: is the 2k drive as seen from recovery console) -
If you now disconnect the 98 drive and make 2k one master, it should boot into 2k. The system drive letter should still be what it was. If all ok, you can now do what you want with 98 drive.
PS. worth making a 2k boot floppy - copy the files ntldr, ntdetect.com and boot.ini to a newly formatted floppy. I'd make the boot.ini look like this:-
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINNT
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINNT="Win2k disk1" /fastdetect
multi(0)disk(0)rdisk(1)partition(1)\WINNT="Win2k disk2" /fastdetect
so you can boot it as master or slave.