Hmm... Another question, How can I keep my legit eshop copy of RF4 while in EmuNand? The easiest (and longest) way I can think of is to let the game download all over again through the eShop and finally make use of the Save Backup option.
Any other way? Like make a 1:1 copy of my SysNand to use as EmuNand?
EmuNAND already is a 1:1 copy. Completely unmodified, in fact. The launcher does its modifications in RAM. If you backed up your SD card before installing EmuNAND, you can just copy the "Nintendo 3DS" folder back to the card (after deleting the new one the 3DS automatically generated post-format). The game should still be on both after restoring the original data. My Zelda was.