I had to move out several directories in order to fix the timeline. I am running on a Linux server and I didn’t need to stop Plex. I only needed to move the offending directories, empty the trash and then move the folders back in one at a time to let Plex rebuild the timeline.
I had to move several directories (most of them) in order to fix the issue. I even had to move many directories which previously didn’t have a problem.