No, it won't delete your old maps. I didn't want to risk enraging certain people by accidentally deleting their maps. You'll have to delete them yourself.

Maemo Mapper will, however, automatically modify your repository definitions so that you don't have to modify each one manually. All it does is append ".db" to any of your cache paths that happen to be directories and not files. You'll get a notice about the automatic modification, and thereafter your repository will start empty.