While updating to AC2.7 the 2560 Bootloader got corrupted and would not work.
I have tried to flash the Arduino Bootloader over the ICSP but have too many errors.
Alot of fustrating time later I have to give up. I tried different Programers , usbasp, usptiny, arduino as Isp. Writing bootloader gets verification error.
I can change fuse to No Bootrst and load a blink the Led program over ICSP and it runs ok but can not load the whole Arducopter Hex over the ISP without error.
I have come to the conclusion that the SPI connections to the sensors is interfering with the ICSP function and that the 2560 can not be recovered .
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Update :
My Avr Dragon programer arrived from Mlaysia and I have a bootloader programed and the arducopter FW loaded now.
The APM spi bus translator is not an issue because the reset line disables it when the ISP programer is active.
Usbasp, tiny etc will not work with Mega2560, In hundreds of google pages this is not mentioned anywhere except for one reference to the usbtiny. The Amel Dragon or AVRispII is required to flash the bootloader on the 2560.
I also found that programs in Application memory can not write to Bootloader memory so my attempts to program the bootloader with an application program did not work.
I could not get the mega_2560 bootloader code in the Arduplane Tools repository to work and I had problems with the stk500v2 bootloaders in the Arduino distributions and eventually found a working bootloader from another site .
It does not flash the APM2 Leds but works 100% using avrdude to upload an works with Arduino upload but have to enable verbose to make it work .