I would say they kicked her out after capping the supercedure cells of her replacement(s). Some hives will do that, kick out the queen or the swarm as soon as the queen cells have been capped. That makes for a longer brood dearth within the hive that is bad for hive growth but a sure winner for varroa control.
If you can't find a queen but see queen cells, do not remove any as that is your queen for this hive.