Check the daycare. If you were breeding Pokemon, you might've put it in there.
If not, there is no glitch where anything can just disappear in a newer game (where you can search boxes), so maybe you released it. Remember, icons in the PC are the same, regardless of shininess. You might've released it while releasing junk ones.
Or someone could've stolen it. If you live with someone who also has a 3DS and Pokemon, they might've traded it to their game.