don’t know what happened on your side. usually a system update does not affect any of the roms.
how did you update?
and from which version to which one exactly?
and what hardware do you use? (RPi, PC?)
Waited for a while then rebooted again.
did the system reboot itself or did you reboot manually? my guess is, that the update process has been interrupted by this rebooting and that has caused your issue.
because if it would be a general issue with batocera, then a lot more people would have reported that.