then provide a button or jumper on the board that would trigger a simple circuit to reset the SAM3X and hold the ERASE pin high for a while? This would allow a user to activate the erase function if the SAM3X becomes bricked, then the native port can be used once again to re-program from there.
It also might not be a big deal if you do fairly benign things that don't necessitate a hard reset while the USB is in use. At the very least, you might try to advise users to close the Arduino Serial Monitor or any program accessing the native port before pressing that button!
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