With the release of the Chibios versions of ArduPilot, one thing was missing, but not any longer. The bootloader.
@tridge managed to create a very easy process to update the bootloader, and the process is quite easy.
Note: If your board is one of the original first batches of the 3DR PixHawk, or can be identified as a FMUv2 or PX4v1 the bootloader is not included on the firmware file, so this procedure does not apply
Connect your board to QGC with the USB cable and choose the latest release version of ArduPilot:
after this (the board reboots) go back to the same screen and tick the advanced check box at the top right corner
after the box is selected you can see a Flash Chibios bootloader button. Press it and done…
If you really, really want to be sure, then download the firmware file from http://firmware.ardupilot.org/Copter/stable/your_board
and flash it manually
then proceed to update the bootloader as above.
And done (again)
Welcome to a full Chibios ArduPilot