uEnv.txt confusion when flashing internal emmc

[Pablo999]

I am re-flashing the internal emmc on my BeagleBone Green board with a Debian image from the site stored on the pluggable SD card.

The instructions I received are to modify the /boot/uEnv.txt file in the SD card image which must be flashed and un-comment the last line : cmdline=init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh

This works and flashes the internal memory as expected. What I don't understand is when I then check the /boot/uEnv.txt file when the image is flashed to the internal emmc, the line is then commented out again. What causes this change?

Also, what is the best way to generate a new .img Debian image with the uEnv.txt already modified? Hence to copy the modified image I have on the SD card. Thanks in advance. 

[Pablo999]