Your games should have transferred... Mine did from one SD card to another.
When I got a new SD card, I put it in to make sure it worked and it made folders for the data. There's a folder called something like "Nintendo 3DS" and in it is a folder which is a bunch of random letters and numbers. I copied the old card's data and told it to overwrite files with the same name, but... I had the newly created folder with no games in it and the old folder with my games, which was named a different bunch of random letters and numbers. It was looking in the new one with nothing in it. So I deleted the new folder to get it to recognize the old data.
--- "Please... never do anything as crazy as that again...." "...I'll think about it."