You don't have to reinstall any scenery, in order to use the >2GB patch. You just run the Stand Alone Addon Manager, and will automatically get the correct version for you FS9.EXE. Just ensure you have the latest version of the installer, the one that always gets the latest version of the Addon Manager from the Internet.
Of course, if you don't also have the latest version of each scenery, you'll need to update that ones as well, but the program will warn you about which sceneries are not up to date.