I'm not quite understanding. Balance crankshaft had been swapped? Not room to balance the crankshaft?
The counterweights on an internally balanced crankshaft are larger. Weight is removed from the counterweights by drilling into them. Nothing is added to them.
We used to balance the rods and pistons of some of the VW engines we put into the kit cars. It's a tedious job, finding the lightest piston and lightest rod, then removing just enough metal from them to make them all match. Balancing matching big and little ends of the rods is the most time consuming. If you should take too much from one, then you must go back and reduce the others that you may have already finished.
Externally balanced flywheels and flexplates get a generic weight welded to them, or sometimes the extra weight is cast onto the flywheel. Then metal is removed around the perimeter, outside the cutch plate contact surface, to make the balance.