How to repair EMMC? won't boot after apt-get upgrade

I wanted to use my AtomicPi (Ubuntu) as a file server with a 12Tb drive I recently bought. Before installing the samba server I did a sudo apt-get update; sudo apt-get upgrade first. Just the regular upgrade, not the dist upgrade.
Unfortunately doing that has stopped my AtomicPi from booting. It gets to the point where it would start linux, clears the screen, and shows only a flashing cursor in the top-left corner. Same happens if I wait the 2 and a half minutes during the boot sequence and manage to hit cursor down during the half second window and select the recovery boot option. Now on a regular hard-disk-booting linux I would put the drive in another system and repair the grub setup or boot blocks or whatever the problem was, or on a raspberry pi I would take the SD card to another machine and repair it there, but the AtomicPi boots off this internal MMC and I have no idea how to manipulate it other than when the AtomicPi has booted successfully!
What is the simplest way to get this system to boot again? In the worst case I guess I can reinstall an OS from scratch using a USB key, but I'm hoping there's a less destructive way?

Thanks,

Graham
(In the meantime I've transferred my 12Tb drive to a Pi4 and built a samba server which is working fine, but I still would like to use the AtomicPi again even if not for that purpose)

I would say you need to put a fresh distro on there, it could be it messed with the chip drivers and screwed it up. I'm actually running vanilla Ubuntu on mine, but it's kinda heavy on RAM(working on adding a big swap virtual RAM chunk).
So yeah, I recommend a fresh OS(with all my experimenting I've had to re-install like 5 times). Another tip- DO NOT press the RTC/BIOS reset! When I pressed it on accident, it took a lot of work to get the BIOS to even recognize the eMMC!

More than likely it's a driver issue. I ran into the same issue MANY times before I finally got my OS working to my satisfaction. I had to reinstall the OS each time

JT Alexander (@jtalexander):
Another tip- DO NOT press the RTC/BIOS reset! When I pressed it on accident, it took a lot of work to get the BIOS to even recognize the eMMC!

Time Bomb Alert! Expect this when the little coin cell battery goes dead.