No, that’s not right.
In the 10 precincts I recounted, 5 matched exactly. 4 had differences, mostly due to challenges, and a couple ballots that were skipped by the machine because they weren’t marked in the ovals that the machine reads, but to humans, it was clear which candidate the voter chose. In those 4, we reported the corrected results from the recount.
And the last precinct had 1 paper ballot missing – the total paper ballots was 1 less than the votes recorded by the machine on election day. After multiple recounts of those paper ballots by multiple groups of people in front of multiple observers, we finally agreed that the machine had made an error and overcounted 1 ballot, so the results of the recount (1 less vote) was the certified total for that precinct.
(One of the poll workers there gave an explanation of how a paper ballot could be counted twice – it jams in the machine, a worker opens the machine to retrieve it, smooths it out, and feeds it through again, without remembering to check the machine tally to see if was already counted before it jammed. We agreed that this was most likely what had happened.)
So in that case, we seemed to be missing 1 ballot. But we had no proof that it was actually missing, and a reasonable alternative explanation for the missing vote.
But in Minneapolis precinct 3-01, they have very clear evidence that ballots are missing. They have 4 envelopes, marked “envelope 2 of 5”, “envelope 3 of 5”, etc. – but “envelope 1” is missing! And the total count is off significantly – 133 votes – from the total on election day. Nobody has any convincing explanation for the discrepancy other than that the ballots were lost. Some possible explanations were suggested, but didn’t work out.
So it’s clear that some (6-7%) of the ballots are missing. Therefore the Secretary of State, following state rules, has ordered them to use the election night numbers, as the more accurate ones. I believe the campaign would still be able to challenge ballots in the ones that are not missing. (But I have heard informally that there were almost no challenges in this precinct anyway.)