I recently had to re-install Win2K Pro over an upgraded version of the same from Win98SE. I thought the overwrite would remove the "Windows" system folder and leave me with only the "WINNT" system folder. It didn't. Now when I boot I get the screen which asks me which system I want to boot. (they both are labeled "Windows 2000 Professional". If I select the 2nd instance it does not boot, so how can I remove the selection for a faster boot?

There is a bootmenu file that is hidden in the root directory. If you set bootmenu=0 in that file I think that will do it.