I'm embarrassed to admit it, but I tried something pretty dumb, and know I need help getting out of it...
It's a little complicated, so I'll try to explain this as clearly as I can.
I downloaded Pokemon Y on my first SD card. I put a lot of time into it, already finding a shiny pokemon, EV trained several through super training, and many other achievements.
I found a second SD card. I downloaded pokemon Y onto this as well, using the same 3DS. I started a new file, played for a bit, and saved.
I put my first SD card back into the 3DS, expecting to pick up from where my first save file had left off. Instead, I got this message: "The saved data is not compatible with this version, so it can't be used. Please refer to the electronics manual."
I don't care about the second SD card anymore, but is there anyway I could possibly retrieve the data from my first play through? I tried deleting and redownloading(with a save-data backup of course), but that didn't work.
I know this is pokemon related, but I feel it's best put in the tech section, considering the circumstances. I'm not asking about anything regarding the game itself, just rescuing save data. And sorry for the unspecific title, it's difficult to explain the situation in one phrase, I'm more stressed out by this than I should be.