Nuts didnt get to this form in time.
There is a much easier way to do that and not format and not reload and all your proggies will still work. . . for future reference:

Boot off the 2000 Pro CD
Go thru the setup as if your going to install a fresh copy.
It will scan for previous installations then ask if you want to repair this installation or install a fresh copy.
Tell it to try and repair, it will reinstall wndows but keep your registry entries and what not.
There ya go windows is fixed and you dont lose any thing.