Revision 2 of SAM4N Xplained Pro is the initial released version.
In backup mode, the ERASE pin will only work with a power toggle of the SAM4N. This however can't be done by the embedded debugger because there is no switch to control the power to the target. So in cases where e.g. an application is in backup mode and the user needs access in order to program/debug it is necessary to do a manual erase procedure.
Workaround:
Connect ERASE test point on the bottom side of the board to VCC (3.3V) e.g. pin 4 on the PWR header. Remove power from the board and reconnect again. The device should be erased by this procedure and it is possible to program/debug via the embedded debugger.