That dog behaviour is the bit that gets me. Animals don't care about misidentifying sounds or talking themselves out of something, they just react. If your dog wanted nothing to do with outside until morning, something was genuinely wrong from its perspective.
Had something similar a few years back at a farmhouse in Norfolk, heavy dragging sound on the roof, no trees nearby, no animals that could've got up there. My mates dog at the time pressed itself against the wall and wouldn't move for hours.
Worth checking the roof in daylight obviously, look for scratches or disturbed tiles. But also - what was the weather like? Still nights with no wind sometimes carry sounds in weird ways and things can seem much closer or louder than they are. Not saying thats what it was, just worth ruling out.
Did you hear it move in a particular direction, or was it more static? And how long did it last roughly?