Check out No Voting Machine Virus in NY-23 Election(from Bo Lipari - Essays and Images:

"Finally, the good news – because New York votes on paper, everybody’s vote was counted. When the scanner stopped working, the ballots were removed and counted, so no votes were lost. Paper ballots, a software independent record of the vote, proved their great value in their very first outing in the Empire State. " ( from: No Voting Machine Virus in NY-23 Election)

Its an interesting article explaining what actually seemed to have happened in NY-23. I say "seemed" because I am sure there must be other interpreations and explanations, but the one I am citing here rings pretty realistic to me.