"An inconsistency in the boot archive was detected and the boot archive has been successfully updated. Rebooting"
After further testing, it transpired that the ABE had been rebooted with the "reboot" command, thus not resulting in an orderly shutdown.
A recommendation was given to reboot boot environments with either "init 6" or "shutdown". Once the ABE had been recreated and upgraded, a subsequent "init 6" avoided any further issue.