You can't get back the save data since the game called it corrupted. Furthermore, to add fuel to the fire, you've started a new save file (I assume), thus ensuring no way to get back all your previously owned pokemon (save file overwritten).
yeah, reformatting the SD card is completely irrelevant to all this haha With most games, what @3dsatackman did IS the right way to do it. I think the reason for the problem here goes back to the fact that for Pokemon games part of the save data is stored within the cartridge itself. With the lack of a cartridge to store that specific part of data, the SD card takes this roleProbably is just as naagza has stated. Another reason could be you did not format the new SD card before passing the files. This is just a measure to make sure it is in the same format.
However if you indeed downloaded the game digitally I really think it is what he said.
I also agree it was a mistake to create a nnew file and save over the corrupted one, as then tehre is no one you could ever link back that. I think you'll have to start over.
of corse in your case you probably wasn't going to do that - thats one reason why i like the psychical copy a lot better - sorry for the loss man - i really hate it when save data gets corrupted especially pokemon - hope you get going in the game good 
hope you do well for the tag battles man - i could give you a protean frokie - to start you off or some strong leveled pokemon to help get through the game faster sorry about the game 
haha i agree with ya chief i always get the cardThat is why I stick with physical copies. You can easily switch between system and SD cards without a problem.
Good luck getting back into the game @3dsatackman though!
i'll get ya a tepig for 8 pc ?