I have not performed the transfer yet. I am just trying to find a way to transfer without losing one downloaded game on the target system. If there is no successful way to do it then I am out one game and that's life.
I think that the eShop accounts of the original and target systems are combined on the target system. So after you do the transfer,and move the original SD card to the new 3DS, you can download StarFox onto that SD card (assuming you have enough free blocks).