Sounds like they swarmed.
Are you inspecting the brood box every week? You should be looking for queen cells weekly during the nectar flow season, and be prepared to intervene if you find them. Otherwise, if you let them swarm, you will lose most of your colony and a lot of your honey.
Do most people in your region use 2 brood boxes on their traditional hives? Most regions in the US do. The Flow hive was developed in a subtropical climate, where they can get away with one brood box. However, it is really just a different method for extracting honey. Everything else about beekeeping in a Flow hive is the same as traditional hives. Traditional beekeepers in my region use 2 brood boxes, so I do too. If you don't, you may have trouble getting your colony through winter.