That's how it worked for me.
I selected "Setup Emunand". Everything that was in sysNand was also in emuNand. (I had purchased a few games off the eShop previously, such as SSB4.)
The two were linked, so CIAs installed in emuNand had the unwrapping bug.
I formatted sysNand, and it got a clean home screen, emuNand was untouched.
Downgraded sysNand, added folders to spell out "SYSNAND", moved everything other than System Settings off the main page.
emuNand still has everything it had before, all my friends are still friends, friend code is the same, street pass is the same, Mii Plaza still has everything, legit SSB4 is present and runs just fine, and so on.
sysNand can no longer see SSB4 and other legit games, and would not be able to run them even if it could, since the signature they have no longer matches the new ID generated for sysNand when I did the format, though.
Did you install/download these items after setting up the emuNands? Installing titles updates the title.db (and I think there's another file, but I could be mistaken) that exists in the internal memory, and not on the SD card's file structure. So anything installed after the cloning/setup will only appear in the nand where it was installed. I believe there are guides for extracting/updating/injecting the title.db and such, but it's not something I've messed with personally, so I'm afraid I can't give much more information than that. It might require the nands to be linked (using the same ID), as well, especially if you're going to be trying to move anything into sysNand.