I too had a pretty bad case of chalkbrood this spring (well, not me specifically, but one of my hives
). They never dwindled but never thrived either, until I requeened.
I think Michael hit it on the head, you have something else going on in there that is smacking the hive down. Very likely whatever it is started before 3 weeks ago, even 6 weeks ago. Queenlessness (although you are seeing eggs..could it be a laying worker..any capped drone comb?), pesticides, mites, etc, they all can cause this to happen. I don't think that brood diseases like chalkbrood will usually cause rapid depopulations.
The dead half hatched bees died from cold.