In the old days, paper ballots would also 'go missing' from districts known to be favorable to the other side (aka be chucked out of trucks on a bridge over a river). The best option seems to be open source voting machines + paper audit. This way you get immediate counts and then an audit trail, so would-be manipulators have to mess with BOTH at the same time which is significantly harder.
Think you know a better way HN? Let's hear it.