If you run Setup.exe from an existing Windows 2000 Pro installation and install to a new folder, Setup doesn't remove the existing installation. In fact, you can dual-boot between the two. It's unlikely that you would want to do so, however, unless you need to test different configurations and don't want to reconfigure the existing installation. Or, perhaps you want to have a backup installation you can use to boot the system if the original becomes unstable or unbootable.
If you don't need both copies, you can remove one. To do so, first edit Boot.ini to remove the entry for the Windows 2000 installation you'll be removing. Make sure to check the path in the entry to be sure you're deleting the right one. Then, change the value of the default entry in the [boot loader] section to point to the installation you're keeping.
When you reboot the system, it will boot to the copy of Windows 2000 that you want to keep, assuming you made the correct changes to Boot.ini. You can check to be sure by opening a command console and typing the following command, which echoes the system root folder to the console:
When you're satisfied that you've booted the right copy, you can open Windows Explorer and delete the old Windows 2000 system folder.
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