If you can on the SD-Card open /boot/uEnv.txt and show the LAST line.
If it starts with # then the eMMc is not being flashed To cause the eMMc to be written remove the # at the start of the line.
After making that change leave the SD-Card in and re-boot the Beaglebone.
If all is good the leds should start blinking back and fourth "Cylon from Battlestar G..."
The unit should power off in about 10 minutes. Remove SD-Card. Re-boot and you should be running from eMMc.
Keep in mind when cloning an image to adjust your IP address settings. You can't have duplicate IP addresses.
Ken