I had a dual boot system with 98 on the C: partition and 2K on the D: (actually 2 separate drives). While trying to manually uninstall some Norton stuff, I hosed the registry on the 2K a bit.
Next I tried reinstalling the 2K, but made the mistake of doing it while logged into 2K (I have the \i386 install files on the hard drive). What happened is that I ended up with a fresh extra 2K system on C:\ (2K and 98se on C: and the original 2K on D: drive). The multi-boot menu had all three selections. Also my registry problem apparently was cured. I could boot to all three systems no problem.
So I removed the new W2000 system by deleting the \winnt and \documents and settings directories, and editing the boot.ini file to remove reference to the new system on partition 0.
Problem is that when the machine boots, there is now still a third system to select, called "Default" something or other, so I have to select the Windows 2000 Pro system manually. I can also boot to 98 OK. I didn't think to try that third selection(it was late last night at home, I'm at work now. Anyone know what's going on with this "default" selection, and how to get back to my original two selections?