I found here a thread explaining (as far as I can understand) that there is now only one version (the microSD version) that can be flashed on the eMMC using:
sudo enable-beagle-flasher
sudo reboot
So if I understand well, all I have to do is insert the SD card, connect via SSH, and type the above 2 lines and the eMMC will be flashed.
If the flasher is not installed, then:
sudo apt update
sudo apt install bb-beagle-flasher
and
sudo cp -v /etc/beagle-flasher/beaglebone-black-microsd-to-emmc /etc/default/beagle-flasher
Is my understanding correct?