Hi There!
My problem is slightly different than you most hear from systemtransfers, but I figured out that you might know the answer.
I recently bought a second hand 3DS XL Zelda Limited Edition with a game code, but the game code
has already been used (BUT there is no sign of a nintendo ID on that system) and
I don't know for sure if the game will dissapear after a system transfer?
I came up with two possible answers myself, but to afraid to try them because I don't want to lose my game....
My first guess was that I somehow connect my nintendo ID from my older (source) 3DS to the zelda (target) 3DS XL and
thus to the game that is on there
OR
I use system transfer en hopefully the game will be on there of somehow can be downloaded from the
download list with my nintendo ID from the older 3DS