I would like to point out that I used the two commands aerofc-force-bootloader-pin.py 1 and aerofc-force-bootloader-pin.py 0 to force the flight stack to go to bootloader. When I tried checking for the version of my FPGA, BIOS, OS and FC, it returned 'unknown' next to AeroFC firmware version.
I'm having the same issue. Unable to update flight-controller firmware.
I found a work-around but it's extremely time consuming. Hopefully someone has a better solution.
Here's how I work around it: Reprogram the FPGA with the recovery version, update flight controller, then reprogram FPGA back to default.
(I shutdown and restart the drone as a precaution after each step)
jam -aprogram aero-rtf-recovery.jam
jam -aprogram aero-rtf.jam
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There is a fix that will be included in the next software release. In the meantime, flashing the flight stack with the following commands should work.