Not seeing all video files

They’re readable to a human, but none of them match the convention in the article.

Plex is looking for this:

  • /TV Shows/ShowName/Season 02/ShowName – s02e17 – Optional_Info.ext

So for example:

Season 1
    The X-Files - S01E01 - Pilot.mp4
    The X-Files - S01E02 - Deep Throat.mp4

Season 11
    The X-Files - S11E01.mp4
    The X-Files - S11E02.mp4

The Special you have in Season 10 is best moved if you would like metadata to be fetched automatically. Here’s the TVDB link for it.

Specials
    The X-Files - S00E07 - Re-Opened.mp4

Another approach people sometimes use with Specials, if they really want to keep them in a Season folder, is to name them S10E00 or S10E107 and manually fill in the metadata as desired.

For the Season 9 file with episodes 19 and 20 concatenated together, you have a couple choices.

First (recommended) is to split it into two episodes.

Second is to just name it like this:

Season 9
    The X-Files - S09E19 - The Truth.mp4

In that case there won’t be an E20 in the library, but everything will just work.

Another choice is to name it like this:

Season 9
    The X-Files - S09E19-E20 - The Truth.mp4

In that case, both episodes will show up in Plex … but when you try to play either of them, both episodes will play. It’s quite confusing.

If you have a significant amount of media to clean up, consider investing in FileBot or TMM.