After making some significant changes to a number of levels, I rebuilt my personal IWAD and was quickly going through all the maps by typing "map mapXX" at the console. I'd take note of any messages I got at the console, quickly look around the map and then move on to the next map.
It just so happens that the last map uses a skybox of the 6 sided GZDoom type. It's also the case that this skybox has a very clear orientation because the moon is shown on one of the sides. What's more, the level has quite a few "shadows" behind structures made by darker sectors. All this made it very obvious that the skybox had apparently rotated by 180 degrees because the moon was now shining directly onto the areas of the map that were in shadow.
So, that's it. I'm not sure if more than just this skybox showed the oddity or if any regular skies had. I just know that the skybox for my final map had rotated (everything was still aligned - so the whole sky had moved, not just one side or anything). The sky is not set to scroll or change in any way on that level. When I quit GZDoom, restarted and went back to the map, the skybox was the correct way round.
Well, like I said, probably nothing really useful here, but at least you know it happened.
