I had similar things going on. I had two different TV shows being identified as duplicates. I splitted them manually, but then marking one’s episodes as watched had the other’s episodes also become “watched”.
I Plex danced both shows… taking them away from where Plex sees them, cleaning all traces within Plex (aka Plex dance), then renamed the individual file names to something completely new and added them back. Plex problem circumvented for me…
