Simply delete the unwanted Windows folder, irregardless of whether it is on the same partition as your wanted copy or a different partition. After you have done that, run msconfig, select the BOOT.INI tab, and click "Check All Boot Paths". After the check is done, click Apply, click OK or Close (sometimes it renames the OK button to Close), and reboot your system.
If your unwanted copy of Windows is on a separate partition, you may want to move all your wanted files off of that partition and format it so that all the Windows files are removed.
