You have not given us your representation of a polygon. So I am choosing (more like suggesting) one for you :)
Represent each polygon as one big convex polygon, and a list of smaller convex polygons which need to be 'subtracted' from that big convex polygon.
Now given two polygons in that representation, you can compute the intersection as:
Compute intersection of the big convex polygons to form the big polygon of the intersection. Then 'subtract' the intersections of all the smaller ones of both to get a list of subracted polygons.
You get a new polygon following the same representation.
Since convex polygon intersection is easy, this intersection finding should be easy too.
This seems like it should work, but I haven't given it more deeper thought as regards to correctness/time/space complexity.