Backfilling the brood as it hatches is a behaviour that is sometimes in the lead up to swarming.
Provided there are enough bees in the hive and they still actually have a queen you can solve both issues like this. Take a few brood combs and put them in the honey boxes, alternating them with the honey combs. Put the honey combs from the honey box down among the brood nest, alternated with brood combs.
This spreads the bees considerably & will encourage them not to swarm, for now. I a week or 10 days have a look the combs among the brood nest should be drawn, a few of them may contain larvae. Swap them back to the original position in the honey box and return the brood combs to the brood nest. You now have drawn comb, honey, and possibly brood in the honey super and the bees will start working in that area.
If you use a queen excluder, throughout these manipulations shake the bees off any combs you lift out of the brood nest to ensure you do not get the queen above the excluder.