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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.
Thank you for your response. It worked this morning and I didn't change a thing. The only difference is that I tried flashing the px4 flight stack first.