So I built a living quarters next to my existing 2 quarters. I went and upgraded it and the rooms joined into 1 big quarter, then my game crashed. As soon as I reloaded the game, the quarters were un-joined. I'm bummed but I think if I upgrade both again they might join up, anyone else encounter this?

Not I! Have you upgraded them again yet?

Well, you can try demolishing the new room(s) then rebuilding them. Rooms can only be built 3x wide, and must all be the same level (uograded) to connect.