Hahaha, I actually did this, and stuff does get weird. Your NNID stuff doesn't fully get transferred and your legit games still won't appear (even if they were installed before), I guess if the NNID tries to connect to eShop from the source (old) console after being transferred, the tickets on the console get invalidated by the server or something. Because they were working fine before the transfer and the NAND backup was right before it.
Other stuff like sharing the same friend code and hosting games from yourself also happen, it's a fun paradox