You can try using PKHeX. You can use your Pokémon DS save, extract the Pokémon from your DS save, and inject them to your 3DS Pokémon save file.I was wondering, with the recent TWL-something hack, will it be possible to use homebrew pkbank (or something similar) for transfer the pokemons from a DS game?
This keeps the Pokémon on both the DS game and the 3DS game.