You probably have a lot of locations that are on top of each other and you disable different layers to show these locations? This is an archaic and inconvenient method, it's much easier to have a location nearby and just move the character there when descending to a new level....
In your case, you don't need multiple obstacle maps. You need to add new objects to the obstacle map when descending to a new floor, and recalculate the obstacle map.
This all sounds confusing, I think a small example with two floors would help explain it better.