Change the episode ordering drop down for the library to TheTVDB and perform a Plex Dance (I know that is going to suck with so many episodes), just refreshing metadata in my experience does little to make those changes actually take. Unfortunately you may lose the customizations you did while performing the Plex Dance, but you probably already lost those when you upgraded to the new agents. Hopefully that fixes it right up.
Edit: You could also try using something like FileBot to rename the files in bulk to TMDB standards but I’m not sure that would fix the bad metadata if it is on TMDB.
