This site, says to...
To turn these images into eMMC flasher images, edit the /boot/uEnv.txt file on the Linux partition on the microSD card and remove the '#' on the line with 'cmdline=init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh'. Enabling this will cause booting the microSD card to flash the eMMC.
No such line exists in the uEnv.txt file. Nor do I see the init-eMMC-flasher-v3.sh
file anywhere on the boot partition, although it may be on the hidden partition (at least hidden to Windows).
I have tried holding S2 (which seems to be an older (maybe?) method of flashing) with no success.
The solution turned out to be pretty simple, although completely not explained.
Simply boot up Debian 8.2, login using debian/temppwd
Navigate to /opt/scripts/tools/eMMC/
cd /opt/scripts/tools/eMMC/
and run the file manually...
sudo ./init-eMMC-flasher-v3.sh
Wait for the process to finish, power off device, remove the SD card and simply power the device back on. It will now boot off the eMMC.