Actually, If you read the instructions(Which i guess you didnt

) that the 3DS flashed on your screen before hitting the blue "Transfer" button, you will know that you have to, after the transfer, copy/back up the source sd cards files to a PC(along with two more options I think) then transfer it into the micro sd card that the target system(N3DS) will be using. I tried transferring an o3ds to n3ds to so I know.