Perfectly natural. My advice is do nothing at this time.
In late summer and fall, the Bees set themselves up in the bottom with resources above. Over winter they follow the resources and the heat conservation, gradually moving up. Thus at late winter, early spring, they will begin their season working from the top down. In this way, at this time, it is normal to find brood above and empty frames below, perhaps even some resources below. As they need it, they will go down to get the resources and bring it up for the brood thus emptying the frames below.
So ... leave the Bees be, for now. You will find and observe that upper brood will be emerged in a month and queen working below. The bees having timed clearing out the upper for when your spring nectar flows arrive. They will fill up there with nectar/honey and move down at that time.
The bees know what they are doing. Your role is to make it easiest for them to do it. At your inspections: clean away debris and dead from bottom board, verify healthy brood and bees, verify queen healthy her pattern and her workspace, then get out. Leave everything where it is. Wrong time of year for manipulations. If you do so now, you will likely set them back significantly. Avoid making work for the bees until they have a strong population and a heavy flow coming in.
IMHO.