Please can you elaborate a bit more?
If the memory is erased and the mcu is reset, then how when i disconnect it and then reconnect it it appears again and works ok?
I 'm not using the serial monitor but a c windows program ( i program this). So when i run it and i have enabled both the native and the programming COM. The reset that is triggered by the initialization of the programming port makes the native port be seen again by windows (without physically plug it and un-plug it). But in this case the native port don't work any more for serial communication.
So in general i'm looking for a procedure to "reset" the native port so windows be able to see it again without loosing the functionality.
Isn't possible to use at the same time both the programming and the native port of the Due for serial communication?