Power fractal shader v3 01, change smallest scale to .1 instead of .0025 of whatever its currently set. Sky and everything seems to render correct again.
A good tip on how to debug scenes like this is easy to do in a few steps:
First just make sure things are flowing correctly, clear out nodes not being used, clean up node view and just see the flow of things.
Now, try to determine whats going wrong. And compare it to the defaults of a blank scene, or the defaults when a node is made.
Going through your scene:
Sky/lighting is messed up... Ok, lets check atmosphere/clouds/lighting. After glancing through them, they all seemed reasonable values, barely anything changed from default, so it most likely wasn't the problem.
Thinking, terrain also can cause odd sky/lighting problems where displacement screws things up. So I first when and disabled all shaders and tested, it rendered fine. So I knew it was in your shaders.
Then I went through enabling them one by one to see what happened. One caused major problems, one didn't seem to cause too much problem, and another caused some weird spikes if i recall correctly. They all had one thing in common (glancing at the node view), that was the power fractal surface shader. Since they seemed to all cause a little something, I decided to start there. Double checking later the rest of the shaders used in there seemed reasonable too, so yes power fractal.
I told it to disable displacement in the power fractal shader, it rendered correct again. So I confirmed it was in this shader. Then I checked the values in it to a brand new default settings fractal shader, and the only thing that was quite a bit different (besides things you can ignore like seed), was that you had the smallest scale set a lot smaller then the default, so I set it to default, and wallah she worked again.