Most of my media files no longer appear

Plex Media Server Desktops & Laptops
9

  1. You will ned to add
    /storage/Media/TV\ Shows/Archive/
    and
    /storage/Media/TV\ Shows/Current/
    individually to the library.

  2. Always add the release year of episode 1 in season 1 to the top folder name of a show.
    (just as you did with “War and Peace”)

  3. always use subfolders per season (even if the show only has one season)

  4. exclude any optional info from the file name, or mark it as “to be ignored” by enclosing it in one pair of square brackets, i.e. instead of
    Dark.Winds.S02E06.1080p.WEB.h264-EDITH[eztv.re].mkv
    use
    Dark.Winds.S02E06.[1080p.WEB.h264-EDITH-eztv.re].mkv

  5. ensure that the user account under which Plex server is running has at least “read” privileges to the media files and folders.

These are the rules: https://support.plex.tv/articles/naming-and-organizing-your-tv-show-files/
Following them will avoid trouble in the future.
(And not only in Plex, because this is naming scheme is understood by pretty much any other media software out there.)

After making the changes, you may have to perform the Plex Dance to make Plex forget the wrong matches of the files to the shows.
If this affects the whole library, it is probably faster to just delete the library and re-create it.