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Just some background info: I have a physical copy of Pokemon Y and have not done any hacking, manipulating, etc with the game. I have done a lot of GTS trades and I released any Pokemon that I suspected were fake. (I don't know if that would affect anything.) I also take very good care of all of my games and my 3DS.
Here's my problem:
Two days ago on Sunday I decided to check on my game as I haven't played it in months. As soon as I started playing I decided to to check on my Pokemon in the GTS and while the game was saving before going online the 3DS froze and I got an error message that told me that I had to reset the 3DS. I reset the 3DS, which took a long time, and when I opened Pokemon Y up again I got the screen that says: "The saved game data is corrupted. Refer to the electronic manual."
I then check the manual and apparently I'm screwed. It lists certain situations that can cause the save file to be corrupted and then it end with "Please be aware that in these cases data cannot be restored."
I am really starting to get scared at this point. I then email Nintendo for help (I still haven't heard back and it's been two days now) and started to see if I can figure it out on my own.
I have tried every recommendation that I could find online: cleaning the cartridge, cleaning the DS, restarting the game dozens of times... Nothing works.
So now I don't know what to do. There is no way that I would restart my game. I've got 200+ hours on it, a nearly full Pokedex and almost all of my Pokemon from my previous games (which included tons of shinies). I feel like an idiot now for moving them, but I wanted to see them in that beautiful 3D!
Does anyone know what I could do to get the save file back? Isn't there supposed to be a back up file that I can access?
I was really looking forward to Omega Ruby and Alpha Sapphire, but I don't know if I could ever play a 3DS Pokemon game again if the save file can just corrupt so easy and there's no way to restore it.
I'm sorry. You're pretty much unable to fix it. Is gone. I'd recommend you to start a new game ASAP and get busy in a new adventure. A lot of people would help you with good stuff in the trading board. Don't let this down your enthusiasm.
Also, is your 3DS full with digital games, apps and such? If not, I'd recommend a full system reset as well, and formating the SD card.