If your rupees just vanished and went into the negatives, taking you from the top of the richest people list to the very bottom, then I happened.
People have been cheating to get rupees. That means if I see a person who has never posted on the forums, with more rupees then me, they will be assumed to have cheated, lose them all, and be thrown so far into a hole that if they do recover, I will know them to have cheated.
Even if you weren't cheating, but do have an insane amount of rupees, I will assume it to have come from one of the few cheating rounds, and it will be removed as well.
In part this is because it isn't fair to everyone else, in another it is because some people insist on donating millions to everyone (which by the way, gets them punished along with you). This destroys the value of the rupees by flooding the market.
Another part to this is that we've been having database problems of late, as you may have noticed, and overly high rupee counts take a part in that as well.
So because of all of this, if you suddenly appear at the top of that list, expect to stay at the bottom of it.