Thank you for your question for eXtension. I am not a post harvest Specialist therefore I have reassigned your question to our Tree Fruit Specialist Dr. Diane Miller. Her contact information is <personal data hidden> and her phone is<personal data hidden> she is located on the OSU Wooster campus. She should be able to assist.

Good luck

Brad

Thanks for the good pictures.  Honeycrisp is a difficult apple to grow right.  You have solved the outer fruit rot issues with your spray program.  Now you've come up with an internal breakdown problem.  What you have going is called 'soggy breakdown'.  It's a problem because you can't see it from the outside.  Likely, this is how it occurred and how you can avoid it next year:  It occurs from putting the fruit into the cooler right after harvest.  It can be avoided by harvesting the fruit and letting them sit at orchard temperatures for a few days (up to a week), then put the fruit into the cooler.  Apparently that outside post-harvest equilibration will reduce the acidity enough in the fruit so that you don't get the internal soggy breakdown.  As already mentioned, Honeycrisp is difficult to get right.  The more fruit on the tree, the less likely you will see this problem, I believe.  Fruit from younger trees are more prone to soggy breakdown.  Anyway, next year keep up your spray program and also let the fruit sit outside for a few days after harvest. 
Diane Miller