We did this system when we first started widowhood /roundabout system, after breeding in the main loft was complete we would move the hens into there own loft and trap them back into it again all week, on the Friday we would let the hens out and trap to the cocks loft and on return from the race they would trap into the main cock loft again, once separated, fly back into hen loft and repeat. Also when the hens are out make sure the cocks can't see out or the hens see the cocks, good luck.