Huge sorting machines drop cards into packs at amazing speed. All you'd have to do is ceremonially place this card into the "rare" pile and watch the machine whirr. No one would be able to tell which of the hundreds of sealed and plastic-wrapped boxes coming out the other side of the machine contains the card.
I guess you'd have a trusted employee come out and insert a magic card into the sorter intermittently for as long as it takes, so nobody knows which batch it's actually in.
