I was in that same situation. Go to the eShop and check the stuff you "bought". If nothing else, it would remember you "bought" the game and you can download it on your 3DS free of charge. This happened when I was transferring Shante, and after that, my other DSiWare transfered just fine.
EDIT: SORRY I HAVE NO IDEA HOW TO READ DURR
EDIT: SORRY I HAVE NO IDEA HOW TO READ DURR
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