Shows disappearing while merging

I think I have understood your issue.

handling tv shows in Plex

preparation

Go to

  • Settings - Server - Agents - Shows - TheTVDB

In there, grab the line ‘Local Media Assets’ with your mouse and drag it downwards, so it ends up being at the bottom of the stack of active agents.
Repeat the same under

  • Settings - Server - Agents - Shows - TheMovieDatabase
  • Settings - Server - Agents - Movies - Plex Movie
  • Settings - Server - Agents - Movies - TheMovieDatabase

doing it right

  1. Look up your show on TheTVDB
  2. Take the title as it is used on TheTVDB. If there is something in parentheses, take that too. If the title contains invalid characters (depends on your file system), like § : % *, simply leave them out.
  3. Check the naming and the folder structure of your show. Name the top folder of the show exactly after the title on TheTVDB. No abbreviations. No additional subfolders. No aliases. Add the (year) in parentheses of when episode 1 of season 1 of this show was aired.
  4. Name the episode files according to the above linked naming guide. Use the same title as for the top folder. Show's Title (year) - s01e01 - additional info.ext (’- additional info’ can be left out)
  5. After you corrected the naming and folder structure, perform the Plex Dance with all files for this show.

There is software out there which can make all those file name changes and subfolder creating for you.
Filebot is probably one of the most powerful of these.