http://beagleboard.org/getting-started#update
This page is missing a step:
/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh
It appears this command is no longer in /uEnv.txt
I'm guessing you could edit that file and add it back before you load the sd card?
##enable BBB: eMMC Flasher: cmdline=init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh
(taken from http://elinux.org/Beagleboard:BeagleBoneBlack_Debian#Flashing_eMMC)
I'm using this image:
https://debian.beagleboard.org/images/bone-debian-8.6-lxqt-4gb-armhf-2016-11-06-4gb.img.xz