From my previous bitter experience with upgrading and the DoT3K, I’d suggest grabbing a spare SD card and putting a completely fresh install on it, then trying that. If it works, consider migrating your old project to the new SD card. It may be annoying and unsatisfying, but if your experience is anything like mine, it’ll be a lot quicker than toiling away trying to fix a broken upgrade.
There seems to be something about upgrades, especially kernel/firmware upgrades, that breaks SPI or something that the DoT3K relies on.
For example after a previous kernel/firmware upgrade, my DoT3K’s backlights & LEDs worked fine but it wouldn’t display text on the display. See: Displayotron backlight problem