You'd need to write the bootloader onto the chip using some external programmer. The empeg itself could do it (after you connect the write enable for the boot block) but you can't boot it without the bootloader...

The reason why it's using the flash is that you've got very limited amounts of power available once it's detected a power fail. You definately don't have enough to keep the drive spinning and then write to it.

The relevant comment in the empeg state driver is:

* This driver handles the emergency flash programming system used by
* the empeg. Periodically the player will write 128 bytes of memory
* to this driver. When the power fails this block is written to flash
* using an algorithm described below. The powerfail interrupt is
* triggered when the input voltage to the PSUs falls below around
* 10 volts - we have a bit of time due to the capacitors on the PSU
* keeping us going!

You should be safe anyway, 6 million or so writes is plenty! (Not the same as 640k is plenty though )