Wow, people are telling really ridiculous stories and ideas here. -.- Here's the thing, that would not happen. When glitches happen they are random. They don't ever do something as specific as that because glitches have neither knowledge nor free will. They are simple natural holes in hex that will always appear to make something totally messed up nonsense, just because nobody's perfect. A bug is an exaggeration of a game's programming that causes a problem that, oftentimes, cannot be avoided. What you guys are describing would never happen the way you're describing it due to a widespread glitch.
If you lost a Pokemon it is most likely due to a cloning issue (which is a bit of a bug) or you just lost track of it. It's not going to disappear from your PC because that is something we would all definitely hear about, considering even the latest game has been out for over a year.
Sometimes I get the feeling I've lost something from my box but it is just my bad memory, or possibly I wasn't looking hard enough. :/