Me, too. I'd like to find out how to do this, too. Not a big deal, but somewhat annoying in that the menu shows everywhere you've ever gone for as long as you've had the program installed to try and pick up a video file to burn. And the list keeps getting longer with most, if not all, of the locations being irrelavent any more. I suppose that I could completely uninstall and reinstall it to clear this history, telling CloneDVD not to keep any previous info, but that's a pain. Just a minor annoyance in an otherwise outstanding piece of software!!
Doing a little digging it appears that information is stored in the registry. I don't know if an uninstall/reinstall will wipe that or not. If you're comfortable with regedit you can wipe it that way. If you're not regedit savvy I would recommend living with it unless Sluysoft releases an official method.
HKEY_CURRENT_USER/Software/Elaborate Byes/CloneDVD2/ InputFilesPathHistory and OutputFilesPathHistory and VideoFilesPath
Just remember if you accidentally FUBAR your Windows registry that neither Slysoft nor Elaborate Bytes accepts any responsibility.