This is only necessary if you have custom artwork or other metadata, want to keep played / unplayed status, etc.
If you do not care about such things, then the best thing to do is Plex Dance the files. It is like starting over. It removes all traces of the movies/shows/etc from your system.
No idea how Plex reacts to hard links. However, is space really an issue? The duplicates do not have to exist for a long period of time. Once PMS scans the libraries and matches everything you can delete the original files.
