The Plex Dance mentioned by dbirch should hopefully do the trick. I suppose with all the back and forth, Plex had already cataloged the files “somewhere” and recognized them (same size, same fingerprint) – therefore it didn’t do a full match.
This is actually a pretty helpful feature if you start fiddling with file names in the future but don’t want Plex to turn your library upside-down. It can be quite cumbersome if you’ve been doing changes to your file names for the purpose of getting them matched properly in the first place.