This will follow closely as the same steps as if setting up a new emunand.
Primary SD card will be referred to as Prime. The new SD card will be referred to as Beta.
On Prime you want to run Decrypt9 and backup your emunand.
After your Emunand is backed up copy all files, including the emuNAND.bin, from Prime to a safe location on your computer.
On Beta make sure you can access homebrew and go through with the same steps you did to setup emunand. This will format Beta, but don't worry as after this is done you will copy all of your files from Prime to Beta, including the emuNAND.bin.
Restore the emuNAND.bin with Decrypt9 on Beta.
Congratulations. You just transferred your emunand from one SD card to another.