If the flavor you want to put on emmc is currently booted from sdcard then take a look at this thread, specifically post#7. Just replace the debian image with the one of your choice. I've done this multiple times without error but to be clear I was only restoring the stock Debian back to the Emmc.
https://forum.pine64.org/showthread.php?tid=8229
https://forum.pine64.org/showthread.php?tid=8229