JakeTheOneDude

Um it shouldn't have gotten formatted, what you need to do is redownload Pokemon OR onto the old SD card and you should be able to load the old save, because I'm thinking you just missed the last step of the transfer process which is to put the old SD card in the new 3DS. Even if the game itself doesn't show up on the old SD card the old data should still be readable from it, which is how you got your save on here in the first place.

Wait all you need to do is put the old SD card of yours in you're new 3DS and you should be good. Also I have no knowledge of PKHeX so I can't help you if that's not the case

Did you put your old SD card in your new 3DS? Because what happened when my brother did a transfer was he thought it would just transfer all the contents of his old SD card to a new SD card, but in reality it just made his old SD card usable on his new 3DS. That may or may not be the case for you but thats what it sounds like to me.