If the file names already contain the season and episode numbers (as per the naming guidelines for Plex), then it is relatively easy to take them from there and put them into the meta tags.
I use mp3tag for this kind of thing.
It has a feature called “Convert: Filename → Tag”
You instruct it with some patterns on what to look for.
For instance, the string %tvshow% - s%tvseason%e%tvepisode% - %title% will transform the correctly formatted file name Arrow - s01e08 - Vendetta.mp4
into metatags thusly:
Alternatively, you can replace all tags which shall not be set with just %dummy%. In this example, only the %title% is useful for Plex. So you could use %dummy% - s%dummy%e%dummy% - %title% instead.
mp3tag is available on Windows and Mac, and can be executed on Linux using Wine.
The other way around is also possible. It can also transform filenames to differently formatted filenames etc.
