You should be able to just split them apart at the show level then fix match which ever one needs it.
I can’t see any show called Mobile Suit Gundam 79 on tvdb or tmdb so that might be why. splitting a show across disks/directories is not unheard of as folks upgrade drives for space and put new episodes on new drive. Those are probably the combination of things that it thought it was same show
In addition to BigWheel’s point:
If you’re using the Plex TV Series agent, you can improve the matching quality by including some more information into your folder names. The Show’s folder name should include the year the show first aired (e.g. Mobile Suit Gundam 0080 (1989)). You can optionally include the ID from The Movie Database or TheTVDb to further improve the matching quality (e.g. Mobile Suit Gundam 0080 (1989) {tmdb-46512})
Independent of using the Plex TV Series agent you’ll generally get the best results if you stick to how those shows are named in the online repositories used by Plex. There, the show seems to be “best known” as Mobile Suit Gundam 0080: War in the Pocket.
Plex will go by similarity of names – if there’s no exact match, it’ll pick the closest match and potentially merge files from 2 separate top-level folders. So naming will always be key.
Adding the year to the directory name perfectly fixed the ‘issue’
Thanks to everyone for the idea. I knew about using the year to separate exact duplicate names but didn’t think it would apply in near matches just as well.