Nothing wrong with extracting honey from frames that have had brood in previously.
If you want to reduce them to single brood without finding the queen, either just split the boxes and have them as two colonies (the half without a queen will raise emergency QC's)
or
Just put another queen excluder between the two boxes. In nine days, the box with the queen will have eggs and open brood, the other box just sealed brood.
If the Q+ box is the top one, just swap them over and have the QX over that (no need for the second now) and leave the brood in the top box emerge - the bees will backfill it with honey.