Biffdebrick is a utility for 'debricking' a Bifferboard, which might happen through inadvertently erasing or corrupting the bootloader.
To use Biffdebrick you will need to have two Bifferboards. The first will act as a JTAG programmer for the other. The 'programmer' will need to have the JTAG disabled for this.
On J1, the 10-way header on the PCB board of the Biffer, connect pins 2-6 on one board to pins 2-6 on the other. That's a straight mapping - pin 2 on the first board to pin 2 on the second, etc... You can optionally leave pin 1 also connected on the programmer board, but make sure you DON'T connect it on the other board. You do not want to connect the two 3.3v rails together on the two boards. When making your cable there is no need to make it particularly short, I have tested this with two old IDE hard disk ribbon cables, and it continued to work with them both joined together in series. That's about a metre length.
Copy a Linux system onto the 'programmer' board. You will need to ensure that it doesn't use the RDC watchdog timer, so unload that module. In fact it should not have any software on it which uses GPIO, as this may interfere with the programming operation. If you want you can use the upgrade kernel and rootfs provided on the Biffboot CE page, that should work without issues.
Switch on the Bifferboard to be debricked, and then run the debrick program:
# ./biffdebrick go
This should result in the latest Biffboot CE version (v3_10 at time of writing) being written to the board. That was chosen as the least-hassle version to use for debricking as it should work with all released Biffferboards, NAS dongles etc..
The debrick utility itself is independent of the flash size. It makes no attempt to detect the flash, and can only write to the final sector. Since this is the same on all boards it should work with anything. If you want to then switch to an alternative Biffboot version or other firmware you can do so after booting the upgrade kernel and rootfs on the board.