What if the contents of the Atmel prom become corrupted?
Power-up the system with the failsafe jumper in the on position to use the Xilinx prom. Then upgrade the Atmel prom in the usual way (the upgrade will complain that the board has no serial number–you can safely ignore these warnings), shut your system down, put the failsafe jumper back to its normal off position, and restart your machine. Once the board is running current firmware you can restore the serial number and the type of the board with “PamControl setConfig”. After this is done, repeat the Atmel upgrade procedure to commit the serial number and the type of the board to non-volatile memory (the Atmel).