Under floor entrance top bee space.
OK, so they'd have to come and go round the sides (or over the top) of the frames.
Which would make 'housekeeping' harder for the mortuary bees... But an underfloor entrance shouldn't get bunged up, even if the rest of the hive was carpeted with dead bees. And we know that if there is any way in or out, the bees will find and use it!
So, I don't think they were ever completely "shut in". (As stated "Bees have been shut in since end November.") But effective ventilation will have been harder, especially once the mesh got covered over with dead and uncleared bees.
Quite a few are waking in the kitchen. I have spread them out evenly under two wet supers. Will see how many pull through amalgamate into one box then put it back under the remaining bees tomorrow. Daft or what.
Presumably the bottom of the frames will have been stuck to the floor, and there may have been the odd bump as they were separated.
So, your 'recovering' bees may be those that detached from the outside of the cluster during your floor swap.
I think its highly probable that the colony will be fine, and that those dead bees were simply normal winter expiry that, because of the lack of under-frame beeway, hadn't been cleared.
Full marks for noticing something unusual, investigating and fixing!
Using a torch plus a "mirror on a stick", one can check the underside of a mesh floor without opening up. Somewhat similarly, with a see-through crownboard, illuminating *under* the OMF can be helpful while peering through the crownboard (usually better than shining the torch downwards anyway!)