Are you seeing cells (royal jelly and larva), or just cups? If these are sealed cells you would really want to leave the largest not the smallest, if your gonna make a queen, it might as well be a good one.
Are you using an excluder? Sounds like you are, if that is the case you need to give the queen more room, like another brood box.
Are you using an excluder? Sounds like you are, if that is the case you need to give the queen more room, like another brood box.
