I see. In that case, this may not get you to where you want to be going.
To back up a little bit... First there was (is) SAM-ba - this is Atmel's system programmer. It supports lots of connectivity modes, but is a pain to configure and is not end-user friendly.
Then someone wrote BOSSA which was meant to be a more specific version, less configurable, and therefore, easier to use for end-users. Both of these were GUI interfaces, but have CLI interfaces as well.
Neither of them work on Arduino, so someone forked v1.2 of bossa, but only fixed the command-line version, and made bossac 1.3a. This is the version that is included with the Arduino 1.5 IDE and will program the Due, but need some special wrapper software to be able to initialize the Due into boot loader mode.
I simply took the 1.3a code and cleaned up the UI a little bit to make it even more end-user friendly and made it able to initialize the Due bootloader. I also made the same changes to the command-line.
So yes, you might be able to use it... but, you will need USB connectivity from your raspberry to the arduinos - which may or may not be feasible. Alternatively, you could use SPI which would allow you instead to use a more straightforward ISP protocol instead of USB->usb emulator->baudrate detector->reset switch->uart programmer that is what is implemented on the Due.
I kind of had the impression that this was far more complicated than it first seemed.
An SPI solution would be ideal however, correct me if I'm wrong, I don't believe the Due supports programming over SPI. I've found a way to boot the Due into it's bootloader through Sketch code so I was hoping to skip the whole "Baud 1200" situation and jump straight to loading the programm.
I wonder if there is a simple way of programming the flash over the hardware serial port? i.e. Load a Bin/Hex(?) file into the Pi and directly send it out through the serial port? Connections between the Pi and the Arduinos are flexible so I'd be willing to try any solution.
Sorry to Hijack your thread. This is something I've been working on for a few weeks and I've had very little replies from anyone.