Just backup your SD card content, before making a emuNAND, and put everything back on the SD card, that way emuNAND will be a linked with sysNAND, but if you want to separate them do this, otherwise every time you go to emuNAND all your apps will be wrapped:
Before you make a emuNAND unlink your console from NINTENDO ID, then backup your SD card content.
Make a backup of emuNAND with emuNANDTool_1.0.3 (just for safety).
Put everything back on the SD card.
Boot into sysNAND.
Go into the System Settings app.
Go to Other Settings -- (click right 3 times) -- Format System Memory.
Click 'A'.
Click 'A'.
Remove your SD Card from your 3DS (VERY important).
Accept any further prompts to format your system.
Go through the setup process after formatting.
Insert SD Card when you're on the home menu.
It'll create software data.
Link your emuNAND back with Your NINTENDO ID
You're done!
OPTIONAL: To check if it's unlinked, you'll see 2 folders inside sd://Nintendo 3DS/
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