I followed the above instructions from dbirch and BigWheel. First I set the scanner to Plex TV Series and agent to Plex Series, and episode ordering to TheTVDB. Second I performed the Plex Dance by removing the Specials and Season07 folders after copying them to a drive that is outside of Plex’s view. Then copied them back after doing the steps in Plex Dance.
All looks fine now. I have only one Specials folder and one Season07 folder with their proper contents and episodes properly labeled! Thanks guys for your guidance.
