Thanks Otto! Turns out my naming structure was a little wonky on these ones, so I made the necessary updates. Then I did the Plex Dance (clever) and got most of them to resolve.
I still have a few that are getting lumped together. Can you explain to me what you meant by the split only being available at the show level and not the season or episode level?
I just could have sworn I had used it on episodes in the past. Seems like it’s the most likely place to have duplicates anyway… 
Thanks!
