Plex handling of chapter markers when the file already has them?

If the chapters are in the file, Plex will use them.
If they are not there, it will try to find the movie in its copy of the chapterdb website.
If it cannot be found there, the movie won’t have chapters in Plex.

If you later acquire a copy of the movie with embedded chapter markers, I’m afraid you’ll have to perform the Plex Dance in order to get those chapter markers recognised by Plex.