That is probably the rough equivalent of doing the Plex Dance on the media. When Plex first consumes (scans) media, it can combine files based on its interpretation of the metadata embedded and file title. If you modify any file or metadata later, it is quite unlikely Plex will start over and trash all the work it has done scanning the file. Unlinking files that were improperly linked or matched badly is a pain to do manually.
So we suggest the Plex Dance, if you do not wish to outright delete the library and start over (which is also an option if EVERY one of your files has been read incorrectly).
