Tried but no answer via chat on Friday. Not sure if they were closed for veterans day but looking at the dmesg logs during the weekend it might be the flash as I saw the following:
[103676.228349] mmcblk0: error -145 transferring data, sector 1032, nr 1016, cmd response 0x900, card status 0xb00
[103676.248512] mmcblk0: retrying using single block read
No real way to test the flash unfortunately as smartctl and other utilities can't access the drive. I might try forcing a fsck on reboot but won't know if that works as there's no console.
Not sure if this is the actual issue but another reason why I prefer replaceable storage. I may try adding my own USB storage with the overlay on it to see if I can bypass the upgrade issues.