In both the interest of saving money and learning how the ATmega32u2 is used as a makeshift FTDI chip/PPM encoder, I plan to make my own APM 2.5+ using the open source Eagle files. The only hurdle I foresee is burning bootloaders on to the ATmega2650 and the ATmega32u2.
I have used the arduino as an ISP to burn a bootloader on an ATmega328P, so I would prefer this method because it is cheap and well documented. However from what I understand the APM 2.5+ has a different bootloader for the 2650 than what the IDE provides. How can I burn this new bootloader while still using an arduino as an ISP?
Next, the ATmega32u2 has a DFU bootloader on the APM 2.5+. I see it is provided in the google code repository. https://code.google.com/p/ardupilot-mega/ How do I burn the bootloader using an Arduino as an ISP?
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Have you checked this post? http://diydrones.com/profiles/blogs/restoring-missing-bootloader-on...
I have to re-flash the bootloader of my APM 2.6 and since I have an arduino UNO I hope I can use it but if you managed to fix yours or have any suggestion, it will be appreciated.