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Plex-Meta-Manager
Python script to update metadata information for items in plex as well as automatically build collections and playlists. The Wiki Documentation is linked below.
Since you have the remux, I'd just keep that, and select the right subtitle/audio stream when playing the file back. The major benefit there is that you don't need to have two copies of the same video stream just for different audio/subtitle tracks. The major downside is that if the audio/subtitles you want aren't the default, you have to manually change it for every episode, so for the best experience I'd combine that with a third-party script like Plex-Auto-Languages (a script that will change the audio/subtitle stream for all episodes in a season/show when one changes) or PASTA (a one-time bulk operation tool).
Since you have the remux, I'd just keep that, and select the right subtitle/audio stream when playing the file back. The major benefit there is that you don't need to have two copies of the same video stream just for different audio/subtitle tracks. The major downside is that if the audio/subtitles you want aren't the default, you have to manually change it for every episode, so for the best experience I'd combine that with a third-party script like Plex-Auto-Languages (a script that will change the audio/subtitle stream for all episodes in a season/show when one changes) or PASTA (a one-time bulk operation tool).
Here are PMM's default images. That's where I got the graphic.