Perform the full Plex Dance - all the steps, not just cleaning bundles.
Also, check and set file permissions, even if they look OK. It is rare, but Synology can show them as OK when they are not.
DSM 6: Make sure the user Plex has at least read only access to the media files.
DSM 7: Make sure the system internal user PlexMediaServer has at least read only access to the media files.
See FAQ 19: Setting permissions to allow Plex access to media files
Important: Check the box for “Apply to this folder, subfolder, and files.”