Plex Server not scanning certain files/folders on QNAP NAS

Add the year and TVDB or TMDB ID to the folder name for each series.

Follow the Plex naming / organizing documents as closely as possible. Use the show names as they exist on TheTVDB.com

This will help Plex match the shows correctly.

Yes. Move both series out of the view of the Plex scanners, perform the Plex Dance steps, return the series to the Plex library one at a time. Wait for Plex to finish recognizing/matching the first before returning the second.