My memory is really horrible.
As it turns out, in updating the mapping of Chione, I completely forgot that the Map Editor file I was using hadn't updated the room types from Liam's original mapping. That is to say, while the ice over the lake is now Air and the flat area before the entry cave is now Drained Soil, the tunnel through the lake went back to being Outdoor Concrete (when it should have been Indoor Corridor) and the random Air spot at the bottom of the lake came back.
Long story short, I've updated the room to remove the unintentional reversions. It should be available from the same link as before, but you can also pick it up here.