2. If it turns out that Obama is ineligible to serve as president, then his ineligibility stands from the moment it is determined
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That is a good point since there is no provision for invalidation due to lacxk of qualification etc...
The U.S. Supreme Court actually botched the decision in that case, though the end result wouldn't have changed anyway. The only difference was that the justices in the majority got it completely wrong and the ones in the minority got it so far wrong that they have no business serving in any government capacity in the United States.
The basic point is that the provisions of the U.S. Constitution stand on their own, and cannot be undone regardless of the "extenuating circumstances."