I can only say that what we common folk with common sense would do probably has no connection whatever with what the bazillion lawyers this would involve would do.
But, off the top of my head, there would be no way to declare the election invalid, because the SOB hadn't been convicted of a felony then. After the inauguration, he'd have to be impeached and removed from office. At that point, the VP would be sworn in as President, just like in the Nixon/Ford days.
But if he were convicted BEFORE the inauguration, (or if it were found that he had been ineligible to run in the first place on citizenship grounds), there could conceivably be grounds for having the election nullifed in its entirety. THAT in turn would cause yet a different Constitutional crisis because the sitting President would have to serve longer than the allowed time until a new election could be held.
Then again, if the Electoral College has not yet fully certified its results, they could simply change their own votes and proclaim a whole different winner.
Any way it tumbled, there would be legal fights for a decade or more.
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