Never done this before but I have a working Due and one I believe doesn't have a bootloader on. I've connected to the SPI ports (minus the 5v) and pin10 from the main board to the reset on the SPI on the blank board. I selected the Due board, uploaded Arduino as ISP and hit Burn bootloader and I just get a message saying : Arduino: 1.8.5 (Windows 10), Board: "Arduino Due (Native USB Port)"
Please select a programmer from Tools->Programmer menu
This report would have more information with "Show verbose output during compilation" option enabled in File -> Preferences.
Some nice instructions that are specific to DUE would be nice. Thanks