I have had my 3DS for about 9-10 months now, and it has been great. Today I was playing animal crossing a lot, and everything was working fine. It read cartridges with no issue and they showed up on the home screen. I downloaded the pokebank afterwards and got that working. When I went to download the poketransfer to get my pokemon from Black 2, Poketransfer would not recognize the cartridge and would send me back to the main menu. I exited to the home menu and the game did not show up, there was just a blank square. I tried putting in several games and none of them will read. I am assuming that I will need to send my 3DS to be repaired, but my question is concerning saves.
I have animal crossing and pokemon y downloaded from the eshop, and I downloaded them before the nintendo network was set up. Will I still have these games when my 3ds comes back, or are they linked to the console? Also, are my saves going to be gone forever if my 3ds is repaired? I have been working on my saves for these games since they came out and I really, really don't want to lose them. Is there anything I can do?