Yes she will fill that shallow with brood but since you already made them swarm they usually will not swarm again. You need to time the shook swarm with your main honey flow. With the colony you use it should be at max population before shaking. Now with a small amount of brood to take care of compared to a regular colony more of the honey goes to you for the comb honey instead of raising bees. When adding more supers do not place the empty ones under the others or you will have many with pollen in the comb honey. Keep the bees crowded so they will finish the sections/frames completely. When I use this method I will place a shallow super for chunk honey(this will usually get some pollen in it) directly above the excluder and Ross Round supers above that. That super will stay there until the flows are over. Since it stays there the wax will be darker from travel stain therefore that is why I use it for chunk honey.