Modify Arduino Due's Bootloader to flash when reset
The Arduino Due bootloader is built-in. If you check the Arduino SAM core there are no bootloader files. There is a firmware file for the ATmega16u2 on the Programming Port. You might be able to modify this to do that (given that there is a LED to flash). 

The alternative solution to a modified bootloader is modifing the init() of the Arduino SAM core. Please see https://github.com/arduino/Arduino/blob/master/hardware/arduino/sam/cores/arduino/main.cpp#L36 or https://github.com/arduino/Arduino/blob/master/hardware/arduino/sam/variants/arduino_due_x/variant.cpp#L372. Blink code as proposed by Majenko could be added there. 

Cheers!