As of Plex Media Server version 1.40.4 (and when using the Plex TV Series agent), it is possible to set the appropriate episode order for a TV series (based on alternate orders available from The TVDB for that series), after it has been successfully matched. This is available from the Advanced tab, when editing the TV show.
Note 1: You will need to refresh individual shows or the library as a whole to see the new available orders.
For example, the show Iron Chef had a different order in the United States. In the screenshot below, we can see the different options available from the Episode ordering preference, when editing that show. In this case, the episode files are named and organized based on that US airing release and so TheTVDB (US) is chosen as the order.
Note 2: If you are using Watch State Syning it syncs the episode itself and may not match the numbering we have as primary in our DB. Meaning if you watch or rate the episode “Sakai vs Bruno Ménard (Escargot)” it gets synced as Season 3 episode 46, not the US order that has it as Season 7 Episode 1
