seriously, it's not that big a deal. If that section of roof is connected to the main roof anywhere then, there's an opening for air circulation and a cat still works. If that roof is Isolated then you simply clear out the nest, poison is more effective than traps (sorry squirrelfighter) and repair the opening they're coming in. If squirrels can get in there's a good chance water can too.
You're gonna need a ladder and a brave heart