I'm assuming you restored correctly, so not sure why you didn't have your original eshop games, but i guess you can worry about that latter and download it again.
Do what williams says.
Install something onto your emuNAND, and see which folder increased size. that would be your emuNAND folder.
Install something to your sysNAND, see which folder increased size, that would be your sysNAND folder.
That 3rd folder would be a result of your attempt to unlink 2x, and is a ghost of your system format. You can delete that as that unused.
Turn on your 3ds, go to EmuNAND, just go to a theme selection menu on the home menu. This make sure there is a theme folder.
After that, go to the computer/SD card, and delete the theme folder from the extdata from the emunand folder(you should know which is which by now) as I mentioned before.
then you should be fine to update emunand.