The SAM3X has a bootloader in ROM that cannot be erased. I'm not sure whether there's an Arduino bootloader as well. The ROM bootloader is activated when the flash is erased...
The datasheet says that an application can reprogram the erase pin (PC0) as a GPIO, in which case it will no longer work as an erase pin, except at reset (ie before the application sets it to a GPIO.)
- 6.6 ERASE Pin
The ERASE pin is used to reinitialize the Flash content (and some of its NVM bits) to an erased state (all bits read as logic level 1). The ERASE pin and the ROM code ensure an in-situ reprogrammability of the Flash content without the use of a debug tool. When the security bit is activated, the ERASE pin provides the capability to reprogram the Flash content. It integrates a pull-down resistor of about 100 kΩ to GND, so that it can be left unconnected for normal operations.
This pin is debounced by SCLK to improve the glitch tolerance. When the ERASE pin is tied high during less than 100 ms, it is not taken into account. The pin must be tied high during more than 220 ms to perform a Flash erase operation.
The ERASE pin is a system I/O pin and can be used as a standard I/O. At startup, the ERASE pin is not configured as a PIO pin. If the ERASE pin is used as a standard I/O, the startup level of this pin must be low to prevent unwanted erasing. Please refer to Section 9.3 “Peripheral Signal Multiplexing on I/O Lines”. Also**, if the ERASE pin is used as a standard I/O output, asserting the pin to high does not erase the Flash.**