I would guess 300-400
Machines are programmed and loaded weeks before the election - Don't assume the ballots were all run in the wee hours. Ballots could be scanned days in advance and the cards read later.
Someone could run 10,000 ballots through a machine, put fresh cards in, and then use the original cards on election night. The cards are not serialized and the chain of custody is easy to attack.
But it would have to be legal to count ballots in advance of election day in order to have the hundreds of thousands count jump, right? And there would be no reason to do that unsupervised in the dead of night.