I have a 3DS with NNID. I made system transfer to a 2DS with Pokemon X downloaded. 2DS were formated, because the 3DS contents transfer. Because the NNID (of the 3DS) I couldn't download Pokemon X. Wait 7 days and made another system transfer, 2DS to 3DS. Everything ok, but the just reformatted 2DS eshop, Pokemon X was not there to redownload. Why? The NNID of the 3DS "erased" the 2DS shop configs? The eshop downloads is not tied to the console?
*The 2DS did not have NNID.