PMS tends to combine two files under one episode... how do I separate them?

I just dumped over 700 episodes of One Piece on my Linux PMS setup, however about 100 episodes were categorized as a duplicate with another season, like this:

As shown in the screencap, ep. 001 and ep. 101 were considered the same while it’s really not.
So… how do I separate them?

Are they Television episodes? If so, you must use episode naming and structure format.

Series/
  Season  n/
    Series - SxxExx - optional title here.ext

Programs such as FileBot and TheRenamer will help you lookup(internet) then rename and restructure properly so this doesn’t happen.

@ChuckPA said:
Are they Television episodes? If so, you must use episode naming and structure format.

Series/
  Season  n/
    Series - SxxExx - optional title here.ext

Programs such as FileBot and TheRenamer will help you lookup(internet) then rename and restructure properly so this doesn’t happen.

Thank you for the answer. But wouldn’t renaming mess with subtitle lookup?

No. From what you’ve shown me, although I would need the full XML of the episode to be 100% certain, your files are dual audio meaning PMS will pick up that information as well as any embedded subtitle streams just as it did before.

If you use external subtitles, renaming the video files will break the subtitles.
Luckily though, Filebot will take care of the external subtitles as well, if you use the right renaming instructions:

@ChuckPA said:
No. From what you’ve shown me, although I would need the full XML of the episode to be 100% certain, your files are dual audio meaning PMS will pick up that information as well as any embedded subtitle streams just as it did before.

Just tried FileBot and it worked rather well. Unfortunately FileBot only downloads from OpenSubtitles.org which doesn’t have the subs in my language so I ended up grabbing a version with embedded subs. However that version is named with Japanese characters (One Piece’s original names). Is Plex compatible with that?

@OttoKerner said:
If you use external subtitles, renaming the video files will break the subtitles.
Luckily though, Filebot will take care of the external subtitles as well, if you use the right renaming instructions:
https://forums.plex.tv/discussion/191687/plex-naming-schemes-for-filebot

Thanks. Yes FileBot worked nicely.
Unfortunately it doesn’t have the subs in my language but it resolved the duplicated eps in Plex perfectly.