all our bees are gone!

Sounds like a classic honey-bound hive. You say you saw the hive swarm once, that may have been the primary swarm with your original queen in it. Then the hive should have had one or more queens in the making. It could have swarmed several times without you seeing it happen each time. Eventually there is no fertile egg to raise a queen from and the hive stops throwing swarms and becomes queenless. The workers carry on bringing in nectar but no pollen because there is no brood, and eventually fill in every available cell before they all die. A honey-bound deadout.

As part of your management program, open up the brood nest and pull frames up into the next box up, this is called “pyramiding” for lack of a better verb. What this really means is expanding the brood nest up and making more room for bees to build comb and the queen to lay. Also, make sure you always have room for your bees to continue building, either by removing honey frames or adding boxes. Beekeeping is really about helping them manage space, and letting them work. Working bees are happy bees that tend to stay put more often, but don’t beat yourself up; all hives swarm for one reason or another and you can always get more bees.

~Tyson