A TV Show Library/
…TV Show Name/
…Season 01/
…TV Show Name - S01E01-E02.XXX
They will show in the library as two episodes. They will draw info from TVDB as two episodes. When Plex plays them it plays the file, you see episode 1 and episode 2, but Plex still thinks you need to watch episode 2. Of course when you play episode 2, you start the file over again, so you have to mark episode 2 as watched.
We cover this on a regular basis ad-nausium, but the BEST way to deal with episodes that have been joined is:
A TV Show Library/
…TV Show Name/
…Season 01/
…TV Show Name - S01E01.XXX <— edit this episode to contain both descriptions - or don’t worry about it.
…TV Show Name - S01E03.XXX <— Plex plays this episode as the next unwatched episode - no funny bidness.
‘Feature Requests’ going back YEARS are already in existence.
Every few weeks a new ‘Feature Request’ is created - nothing is done.
Irate Users show up and ■■■■■ about it - nothing is done.
Irate Users threaten to leave Plex - go ahead - Plex doesn’t care - nothing is done.
Use one of the two methods above.
If you use method one - watch the joined episodes and mark the next episode as watched - manually.
If you’re a Fan of that Wonderful AutoPlay, as soon as you watch the first episode you’ll get the same episode rammed down your throat automatically. Sound Good? Oh yea, Man… it’s great!

Most of us just use method two. We know nothing is going to be done, but it’s easier then marking what Plex thinks is an unwatched episode, watched, in order to continue.