Remove 1 show from your primary library, do the Plex Dance, but do not put it back. Instead create a new directory call it TV_Test_Library or something similar, and move the show there, and let plex scan/add it.
Im going to bet it takes far less time than you expect to clean up your library. I can process 1,000 movies in less than an hour. TV shows tend to take a bit longer per show, but the per episode time is minimal.
