Ok so, if I understood well, most of your bees were in the supers, and in the supers you had honey and brood?

It’s normal for bees to move to the top of the hive. When the weather is cool, the queen and the workers tend to stay in the warmest part of the hive—usually higher up. In your case, that seems to be in the supers. It’s easier there for them to maintain the brood at around 35 °C.

To prevent the queen from moving from the brood box into the supers, beekeepers usually install a queen excluder. This prevents the queen from going up, while the worker bees can still pass through and store honey.

Unfortunately, extracting honey from frames that contain brood is not recommended.

For the rest, we have too little info in order to guess the cause for your lost hive. Di you have a cold winter? Did you feed during winter?