I could be wrong or misunderstanding your issue but I suspect what you are talking about is played status/history which is not to be confused with watched status.
Marking something as “watched” no longer creates a “played” entry for it, something actually has to be watched within the Video played threshold for it to register as actually played. This change came in server version 1.40.0.7998 → Plex Media Server - #612 by drzoidberg33.
Again, if this is not what you mean then feel free to ignore my comment.
