I can only speak for New York State (which used a paper ballot that is then fed into a scanner by the voter for tabulation), but the paper ballots are generally

I can only speak for New York State (which used a paper ballot that is then fed into a scanner by the voter for tabulation), but the paper ballots are generally sampled and checked against the "electronic" votes. They'll manually count enough paper votes until they have a match to the machine counted votes (within some acceptable confidence interval, obviously).