I have to remove unavailable tv-show files manually

  1. Edit the library
  2. go to the Add Folders tab
  3. ensure that every folder path on this tab is
    a) existent
    b) accessible to Plex server
    c) not completely empty

If that doesn’t change anything, repair the database files:
Stop Plex server using its task tray icon
open a command line window (cmd.exe) and run this .bat file: https://github.com/ChuckPa/DBRepair/tree/master/Windows