If you Uninstall & Install to the same location it should not affect your addon aircraft. You would have to reactivate any 3rd party scenery from the Scenery Library. You should back up any other important files before doing it.
If you have enough HD space the alternative is a duplicate install of FS2002. Rename the FS2002 main directory folder to any other name. Then insert CD-1 & install in the usual way. You will now have 2 separate installations of FS2002. The last one will be a virgin install & should work properly.