As far as I knew, the only way to lose Pokémon that were transferrable to modern games is to try to clone them in Emerald. Were you trying to clone them in Emerald? If not, how did you lose them? --- For those of you starting topics about the PS4, there's a PS4 board: http://www.gamefaqs.com/boards/691087-playstation-4
I feel there's something you're not telling us, like you're using a ROM/flashcart or you were using an AR.
Nope this is the full story. I usually have trouble with finding pokemon, but eventually find them, but after searching for about 5 or so minutes of going through your boxes for a 15th time there's something up.
I remember when my Skuntank got baleeted, I was explosion training bred pokemon with audinos. I memorized the box and place I left him. Gone. Without. A. Trace. --- "Posts don't have to be on topic if they follow the flow of conversation." -Baseman Moderator