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This is wrong.

You can move your digital library to the new machine.

Nintendo does this for broken systems as well as DSi to 3DS.

Just call them and have your serial numbers handy for broken systems. For DSi to 3DS, its built-in to the 3DS and there is an app to download on DSi.

However, hopefully they'll fix this and tie it to your new Nintendo Network ID vs your machine ID. It would just be simplier.