Nintendo will release a save data transfer tool for the Nintendo 3DS in Japan this March (via: Nintendo World Report). The tool, which will be downloadable from the Nintendo eShop, will allow 3DS owners to transfer save data from 3DS game cartridges to the download versions of those respective games.
Additionally, Nintendo have also announced that they’re bringing more retail 3DS games to the eShop in Japan.
Fire Emblem: Awakening, Culdcept, Pokémon Rumble Blast, Pocket Soccer League: Calcio Bit and Nintendogs + cats will be made available for download by the end of the month.
Nintendo have not announced the save data transfer tool for a U.S. or European release yet.