that sucks. some hives are like that.
when you check again, see how many bees are in there and if there are any swarm cells. if there are still a lot of bees and there are swarm cells, you can either move the swarm cells and a couple of frames of brood (with bees) to a new box, or (and i prefer this) move the queen and a couple of frames of workers to a new box.
my theory on these multiple swarm hives is that they let to many queens live. instead of just keeping one, as most hives do after a swarm, they keep several and end up swarming over and over. if you split the hive, watch for the new queen to start laying. then i would make sure there are no other queen cells made or being made. i know this goes against CW, but you want to try and break the swarm cycle. the worst that will happen is that you'll have to combine the hives again.
also watch the hive with the old queen. hopefully they won't feel the need to swarm if the size of the hive is reduced.
if there are not enough bees, you can boost the hive with frames from your other hive, or combine the two.