Had something similar last year up in Cumbria - weird shuffling/dragging sound on the roof around 2am, and my border collie Meg absolutely refused to budge from under the bed. She's not a nervous dog at all normally, so that got my attention pretty quickly.
First thing I'd rule out is the boring stuff - foxes are notorious for this, especially urban or semi-rural areas. They're heavier than people think when they're clomping around up there. Squirrels and birds too, though they tend to sound lighter and more erratic.
That said, the dog behaviour is the bit that sticks out for me. Animals picking up on something before or beyond what we can detect is well documented in paranormal research. Meg wouldn't settle until about 6am and then acted completely normal after that - almost like whatever it was had gone.
Worth asking:
What time did it start/stop?, Did it sound like footsteps with a pattern, or more random?, Any EMF spikes if you had a meter running?
If you've got a Mel Meter or even just a cheap KII, might be worth leaving it running overnight and checking the logs. I'd also set up a basic trail cam on the roof if you can safely access it - rules out the physical stuff at least.
What's the surrounding area like? Near woodland, water, anything like that? Location can tell you a lot.
Don't dismiss it just yet, but don't assume the worst either. Start with the evidence. 👀