While you’re waiting for the cavalry, I’m curious if any of these episodes are being matched as duplicates of other, existing episodes. You can check in the Library view of your TV library by selecting “Episodes” from the view selection and then “Duplicates” for the filter:
If things don’t look correct there, you can try the Plex Dance on the offending episodes to see if that helps. After clearing caches as @JuiceWSA suggested, of course.
And at some point, logs (with debug enabled and verbose disabled) will likely be necessary.
Take… The Fosters out of the library to a hiding place Plex can’t see (a Holding Folder on the same drive will be an instant success) The whole thing. Whisk it away. The Fosters has a 3. Let’s do that one.
Note what happens, if anything good…
If not - get those logs that captured the Plex Dance and drop the zip on a message window.
Troubleshooting - Download Logs <—they’re in your system downloads folder.
THEN we’ll have something to show management…
(right now @casaal is probably finding out how long it takes to delete 98 million little files…)