i made into copying the bootloader from the atmega16u2 of the arduino due(or at least i guess i made it)
using an arduino uno as isp i wrote on the CMD the following line:
your_path\arduino-1.5.2\hardware\tools\avr\bin>avrdude.exe -C avrdude.conf -c arduino -P COM9 -b 19200 -p m16u2 -vvv -U flash:r:bootloader.hex:i
this is totally different from the one assumed to be the right one in the IDE folder.
did i get wrong reading the firmware from the arduino due board or the hex file given in the IDE is not the one that should be?
i don't have another arduino due to try. please let me know