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
Let’s go:
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
