maybe the patch corrupted your old deck..... i don't know which yugi are you talkin about, but if u have Yu-Gi-Oh! Yugi the Ddestiny "The Power of Chaos", i have a super cool deck that i can email you
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P.S. in that game, my deck has also dissapeared a couple of times..... at first, i got pissed...... later i got over it as i got better and better cards..... the more decks you switch the better cards you get sooner (not neccessarily true)