Just leave out the special chars in the file names. Don’t replace them with other chars.
The scanner should still be able to identify it, provided the file name follows the recommendations:
https://support.plex.tv/articles/categories/media-preparation/
Sorry, that is sub-optimal, to say the least.
Having several thousand files in one single folder will definitely slow down operation of Plex.
I strongly recommend creating subfolders and use the ‘one subfolder per movie’ approach with movies.
Use the prescribed folder structure for tv shows.
Always go with a nested folder structure of Music > Artist > Album > Songs with your music.
Filebot for instance will automatically purge invalid characters in the course of its renaming.
