For eShop games you can call Nintendo and they can transfer the licenses (I did it when upgrading to a New 3DS.) For me the real bummer was that your saves are

For eShop games you can call Nintendo and they can transfer the licenses (I did it when upgrading to a New 3DS.) For me the real bummer was that your saves are also tied to your console and it's more complicated transferring those. I don't mind paying 30-40$ for another game license, but it really hurt losing 100+ hours of progress in several unfinished games.