As noted at the bottom of the eLinux article, there is a much easier way if you are running the Debian distribution:

1. Boot master BBB with no SD card in
2. Insert SD card
3. Log in (e.g. with serial terminal, SSH etc.) and run sudo /opt/scripts/tools/eMMC/beaglebone-black-make-microSD-flasher-from-eMMC.sh. LEDs will flash in sequence whilst SD card is being written.
4. When the LEDs stop and the script terminates, remove the SD card.
5. Insert SD card into new BBB then power on.
6. eMMC will be flashed; LEDs on new BBB will flash in sequence until complete.

For anyone else that needs this, the best answer I've found to this is to do the following:

First setup your master Beaglebone Black the way you want it.

Backup the eMMC

• FAT format a 4GB or larger SD card (must be a MBR/bootable formatted microSD card)

• Download beagleboneblack-save-emmc.zip and extract the contents onto your SD card

  Note: this is an image from Jason Krinder at his github https://github.com/jadonk/buildroot using the save-emmc-0.0.1 tag

• Put the card into your powered off Beaglebone Black
• Power on your Beaglebone Black while holding the S2 Button
• The USR0 led will blink for about 10 minutes, when it's steady on you have an SD card with a copy of your eMMC in a .img file

Use the eMMC to flash a new Beaglebone Black

• On the SD card edit autorun.sh

  #!/bin/shecho timer > /sys/class/leds/beaglebone\:green\:usr0/trigger dd if=/mnt/<image-file>.img of=/dev/mmcblk1 bs=10Msyncecho default-on > /sys/class/leds/beaglebone\:green\:usr0/trigger

  where <image-file> is the image file you got after copying backing up your eMMC

• Insert the card into your powered off Beaglebone Black
• Power on your Beaglebone Black while holding the S2 Button
• The Beaglebone Black should go into rebuilding mode and within about 20 minutes you'll have a newly flashed Beaglebone Black (when all 4 USR LEDs are solid) with a copy of your original

eLinux reference used for this article - http://elinux.org/BeagleBone_Black_Extracting_eMMC_contents

I have the same need and am using dd and nc (NetCat) to save directly on my desktop without having to use an intermediary SD Card. You can do this over the USB connection, or ethernet connection, by changing the IP address in the steps below.

After setting up your BBB with the applications you want, the basic steps are:

1. On the desktop, run this command in a terminal:

nc -l 19000|bzip2 -d|dd bs=16M of=BBB.img

1. On the BeagleBone Black, run this command in a terminal (you can SSH into it, or do it directly from the BBB):

dd bs=16M if=/dev/mmcblk0|bzip2 -c|nc 192.168.7.1 19000

The 192.168.7.1 address is for the USB connection. (BBB is 192.168.7.2) If you're doing this over an ethernet connection, you should use your desktop's IP address.

This is taken from instructions here.

Finally, follow any method to install onto the next BBB. Here's an example of how to flash the emmc.