To me that is exactly what should happen. You told Plex that you wanted those items marked as played therefore Plex so marked it and placed the correct flags in the history. Plex has no way of knowing that you do not want any particular “played” item treated exactly like any other such item.
To Plex it does not matter how an item was moved from “not played” into “played” it just matters that it was so moved and. again for me, that is exactly what I would expect.