You are using Arduino DUE Board, but you not using using the Arduino IDE. Then, how do you store your new application program codes into the flash of the SAM3X8E after the deletion of the the previous program using the ERASE Button?
BTW: What have you wanted to mean by saying 'Boot-loader comes online?
(Under Arduino IDE, the Boot-loaded executes interactive session with the IDE and uploads the Intel-hex formatted application program codes (the sketch) into the targeted flash area of the MCU.)