I don't know how to transfer it but Nintendo has information on their website.
I bought another digital copy for the NEW 3DS so didn't do the transfer. Make sure to buy a larger micro card if you have more digital copies.
I've read a lot of posts where the only game that didn't transfer was ACNL. They ran out of space and lost their town.
Read that the SD card is not equal to the micro card. Micro card holds less.
im getting a new 3ds too soon :0!! i have a physical copy of nl but my hhd game is on my 3ds digitally. would that happen with happy home designer too?