This usually happens when a clipped queen cannot fly with a swarm and goes under the hive; the bees stay with her and the brood nest develops. Do you have a laying queen in the hive or queencells or something else?
Note that bees can pass food through the mesh floor and pheromones can pass through too, of course.
My suggestion is to move the brood box off, move the hive floor and replace the hive floor with another if you have one and put the varroa tray in place to stop flyers congregating there again.
For the bees under the hive floor, you may decide to cut the comb off and discard it or fix it inside un-waxed frames with elastic bands or insulating tape, depending on the size of the comb.
If the original hive has sealed queencells, you may consider housing the "underneath bees" in a hive on the old site and moving the hive with queencells to one side; this is in essence an artificial swarm of course.
I am speculating here - your situation may be different to my 'best guess' - so please tell us more!
May your bees read the same books as you do.