I think they also swarmed while I was at school. There has been a MAJOR break in the brood cycle with nothing but eggs and capped pupae.
Your explanation makes sence if this have happened:
-A swarm left and half bees went. That is normal.
- Egg laying queen went with swarm and you have no larvae.
- New queen has started to lay eggs at the age of 9-10 days.
- After couple of days you shoud have larvae and near eggs you see the fat queen.
You have perhaps varroa and it violates brood. There maybe some another difficulties in brood area like sac brood ?
When field bees went with swarm the rest bees have consumed missing honey to feed larvae and themselves.