I just formated the emunand and moved everything back, but the eshop games won't show up. Did I do something wrong.
hmm... did you restart the 3ds before you put the files back?
i did it today, i dumped my nand. backed up all the sd card stuff on my computer.
then, i formatted emunand. as soon as it was done, i powered off. i copied the files back to the sd card.
then i started up, and everything was fine.
i think if you start up with a blank sd card, then the 3ds will use a different folder id, and... well, i don't know so much about it all to be honest, i have only done it one or two times.
just, that above is how i did it myself today, and it was fine.
maybe if you did start the 3ds with a blank sd card and let it create the folders itself, i think it will still be ok. just copy them back in the same place, inside the new folder in 'Nintendo 3DS'