Gas ports in pistons connect the top of the dome to the back side of the top ring groove. They assist in sealing by forcing combustion pressure to the top and back of the ring, helping the ring seal against the cylinder wall. If the cut is into the back side of the top ring groove, you might just consider it a partial gas porting job, and run them as is. I'd be more concerned with the thickness of the dome in the flycut area, you don't want that below about 0.200". If the pistons are thick enough there, you are probably OK as-is, if I understand the issue correctly...