This message was posted on behalf of Intel Corporation
That is very strange, do you get the same output if you try to flash the px4 flight stack instead of the Ardupilot? I just tested both with Ubuntu and I did not run into any issues.
It seems that the flight controller is failing to boot into the bootloader. Try to run the command with sudo aerofc-update.sh nuttx-aerofc-v1-default.px4 (or ardupilot). If that does not make a difference, make sure the flight controller is firmly attached to the Aero Compute Board.