I once again redesign my whole room spawner, replacing the pre-baked room prefabs with practically empty objects that spawn in the room segments, to maintain a connection to the prefab segments. That way, even if I screw up again, I don't have to systematically go through EVERY ROOM, replacing everything again.
Of course, everything broke again. Then I got mad, then I had a popsicle. And then I passed out in the snow. Then I woke up and resolved the glitches.