Some additional info.
My guess is this happening because plex is changing the guid of the episodes, on a reorder! Looking in the DB itself (I’ve various backups I’m using as reference) I can see in tables metadata_item_settings and metadata_item_views the guid’s of the episodes swapping around and I’d say this is messing up the played/unplayed status.
Anyhow, I’ll just go and run a fixup, just wish plex was more tolerant of cases like this. The episode itself has not changed, its only the order of them.
EDIT: may also be somewhat related to this Changing a previously played episode/show/movie to unplayed deletes the data from dashboard watch history which is another huge annoyance I have with plex 
