Lazybkpr says, "... Spotty brood, empty cells that are refilled with eggs... I looked deeper, and found larvae that was dead and brown.. some of it tiny, some of it a little older, none of it even close to be ready to be capped. I remember seeing this before, and thinking it was chilled brood because we had a few COLD nights early in the summer.. now I am not so sure, but I do not know what to make of it...
Both of these hives had these patches of dead brood.. I have seen AFB and checked or it.. I know the smell... this si not it... I have seen EFB and the rotten smell is something that sticks in my memory and is one of those things you cant UN remember... I have never seen sac brood, but this does not seem to match... It LOOKS like chilled brood.. dried up royal jelly and dead larvae... the bees remove it, and the queen re lays in those cells.... Less than 10% of the cells have been capped.. I opened some of those cells and found live viable larvae/pupae in them... SO, still looking for ideas, with the added information..."
My gut feeling says that there is some sort of disease behind this issue. As much as I don''t like to use antibiotics, in this case I would suggest applying terramycin in a powdered sugar mixture across the top of the supers, between the top bars of the frames.