Rooms were removed leaving a lot of rooms unconnected

Don't think this should be possible; Accidently merged chains, but placed locks so the only possible outcome should be to remove the merging room. However most of my in between level 3 spymasters and a few legion barracks where removed after closing temple leaving a whole bunch of unconnected rooms. 75 rooms, 16 where removed (destabilized), but only 20 rooms are reachable.