The 'mtd' subsystem of the linux kernel has a map of the flash which it prints at boot time:
... SA1100 flash: probing 16-bit flash bus Amd/Fujitsu Extended Query Table v1.0 at 0x0040 number of CFI chips: 1 Using static partition definition Creating 3 MTD partitions on "SA1100 flash": 0x00000000-0x00010000 : "boot firmware" 0x00010000-0x000e0000 : "kernel" 0x000e0000-0x00200000 : "initrd" ...
The mapping from flash sections to mtd devices is as follows:
mtdblock0 00000000 - 0000ffff blob boot loader mtdblock1 00010000 - 000dffff pboot loader (kernel) mtdblock2 000e0000 - 001fffff ramdisk (unused)
The primary boot loader (blob) and secondary boot loader (pboot) can be updated from linux as follow:
cat blob >/dev/mtdblock0
cat pboot >/dev/mtdblock1
sync
It should be pointed out that if this operation is interrupted or fails you may have to go back to the jtag program and use the jtag buffer board to reprogram the flash.