To my knowledge I’ve not experienced this issue and still have Honeycrisp in storage from Sept. 12.
My wife though DID describe to me a condition similar to what you are describing in just 4 apples she found, all were among the larger apples. For reasons unknown to me, this was the first year that I never had any bitter pit. All my apples, save for the few dozen I still have were never cold stored.
Rob, could those apples of yours have had water core before they were placed in storage? Maybe that’s what you are saying, but I’m understanding this to be something different, is that right?
ACN scored HC highly for storage. I don’t remember the exact (I think 6 or 7) rating and they have changed their website and no longer show that info. I personally haven’t been successful at storing any apple for longer than a few months. Mine have never been any better than the day they were picked.
Rob, I’ve also never seen any red swirling inside HC, I’ve seen it a lot in other varieties, but never in HC. Not in any that I grow, or in any that I’ve purchased. I too would be very interested in hearing what causes this pigment inclusion. When I get some more time I’m going to see if I can find anything. I posted a study a long while back that studied red expression in flesh, bark, and stems in apples and it was drawn from one specific allele in a strain of crab if my memory is correct (and it may not be).