Custom metadata for non-standard versions of TV episodes?

Plex Media Server Metadata & Adding Files
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2

build a completely separate folder structure for the same show:

/TV Shows
   /ShowName
      /Season 02
         ShowName – s02e17 – Optional_Info.ext
         ...
...
   /ShowName [alternate]
      /Season 02
         ShowName – s02e17 – Optional_Info.ext
         ...

Once you have organized your files in this way, you can use “Split” at the top (show) level. Which will give you 2 separate posters of the show.

You use the Plex media info to determine which is the one for which you want to use your own metadata.
You then “Unmatch” this version (again, at its top level).

If your files are using the mp4/m4v file container, you can embed the episode titles and descriptions into the files themselves, as embedded meta tags.
Plex will read and use this info.