He linked the 3DS eshop account to his WiiU eshop account to use a common wallet to buy games either for 3DS or for WiiU.
You can't link more than one 3DS to your WiiU-eshop account.
He want to link the new 3DS, but he can't, as there's already one activated and linked to his account, and there's no way to unlink it.
Only Nintendo can do that, so contact them.