Fluke, it happened to me by accident in a trade about a month ago, so it's likely still possible (unless a recent patch did something, but I doubt it.) I don't know what kind of DS the other person was using. There hasn't been an issue with cloning this way before, provided that you disclose that you use it.
MegaSimon, the glitch requires precision timing, so the odds of it happening are low, but not impossible.
Alpha_Arrowz and
Fluke, losing the junk Pokemon and cloning the original are one in the same (you can't do one without the other). Which one gets deleted essentially depends on who loses connection first. If you know what you're doing, you're probably fine and won't lose the original. As for it corrupting your game (in case anyone has that question), I suppose anything is possible, although again, the odds are really low of that happening. :)