As a follow up, I was getting about ~50 unfixable chunks in the same areas in the last few runs of fixing I did, so I was gonna give up for the night. However, I did notice for some of the stuck hashes the expected and current hash were the same...
Not sure if this is a useful datapoint:
Without having read the recent updates about sleep mode, I inserted my Persona Q cart on Friday and left my 3DS on the home screen in sleep mode up till about late Sunday. When finally I went to play it, it...