what's weird is that when the PC is connected to USB native port of Arduino Due, and the SAM Chip is erased, the PC sees the Arduino Due board as "Bossa Program Port", not SAM-BA.After a sketch is uploaded the Arduino Board is reset, and at that point the PC unplugs the Bossa Program Port device, and the PC sees the Arduino Due as a common USB composite device, with its own COM port named "Arduino Due'.The moment the Flash is erased again by pushing the "Erase" button, the PC sees the board again as "Bossa Program Port".
I think that's normal behaviour for the Due's native port. If the SAM3X8E's flash is erased, either by connecting to the native USB port at 1200bps or pressing the erase button, the Due switches COM port from "Arduino Due" under the control of the Arduino core to "Bossa Program Port" that's controlled by the SAM3X8E's bootloader.
Unlike other Arduinos the SAM3X8E on the Due has a factory burned bootloader that allows the microcontroller to be programmed via its native USB port.
Can I use JTAG interface and Atmel Studio to program custom SAM3X8E chip The answer should be YES or NO. I can't believe that it is so complicated to upload the code on the chip!?
what I can't understand is why the bootloader inside the SAM3X8E, that should be SAMBA, appears to be BOSSA that is an opensource bootloader and shouldn't have nothing to deal with SAMBA.