Starting from version 2.3 the program FLProg added support for Arduino DUE boards. But in the ArduinoIDE package included with the program is not by default loaded packages for this Board.
To download these packages should do the following steps.
Bet you compile the project, after the opening of the window to open ArduinoIDE Manager boards.
Manager boards to select «Arduino SAM Boards (32-bits ARM Cortex-M3) by Arduino»
Click “Install”. After the installation click “Close”.