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.
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