I currently have two games registered for my Pokebank, Pokémon Y and Pokémon Omega Ruby. I transferred ALL of my Pokémon to the BANK and then reset my Omega Ruby Game. Had not touched the Y in a long time.
After resetting my OR I attempted to access the Pokebank to get some of the Pokémon back. It produced an error for me saying: You previously used a different copy of Pokémon X, Pokémon Y, Pokémon Omega Ruby, or Pokémon Alpha Sapphire. Please try again using PokePop's Pokémon X, Pokémon Y, Pokémon Omega Ruby, Pokémon Alpha Sapphire game (Trainer ID No. %number%). Then the game disconnects from the internet.
I then attempted to connect to the Pokémon Y game I have and have NOT reset and it gives me the same error message.
I have contacted Nintendo support three times on the issue. One of the agents didn't even know what PokeBank was and that Nintendo made it. We had to argue about it until I sent him to the Nintendo web site to show him. Then he said, I am sorry, I don't know what to tell you. WTH! You are support!
I will be calling in to day again hopefully during business hours I will find someone with a little knowledge how to fix this.