I have a BBB which has the eMMC flashed from the microSD card using the flasher script. Therefore, the MLO and the u-boot should be idenitical.
Referencing the eewiki page[1]I backed up the MLO from the eMMC and the microSD:
sudo dd if=/dev/mmcblk0 of=./mmcblk0_MLO count=1 seek=1 bs=128k
sudo dd if=/dev/mmcblk1 of=./mmcblk1_MLO count=1 seek=1 bs=128k
The shasums are however different:
debian@beaglebone:~$ sha256sum mmcblk0_MLO
493f8723705c73c3383898658ce2b1855bbca219825198d2a23b115ce30a4ada mmcblk0_MLO
debian@beaglebone:~$ sha256sum mmcblk1_MLO
51d7b68ec8eac56f6d04371c77885332e9eedc7c5434350750ba58f51e86fd56 mmcblk1_MLO
Am I backing up the MLO correctly?