This is a game breaking bug that happens quite often. Any ruler (I think its random) will take over and reform a defeated faction, making him/her a ruler of two factions (Ex: Edmure Tully will reform the defeated Reach, therefore making him ruler of both the Riverlands and The Reach) and he disappears.
Can someone get me a screenshot of when this happens? That will make it easier for to find the correct menus/text etc in the modsys files.