I am intrigued by the mechanism of ballot recounts. In Wisconsin, for example, this NPR article quotes a spokesperson, Murtaugh, who claims that some ballots in Milwaukee County had been "cured" by poll workers, tainting those ballots. Murtaugh estimates 15-20% of the Milwaukee County ballots were thusly tainted.
In looking at the pictured vote tabulator (which happens to be a ES&S machine), one can readily see that there are three bins into which the scanned ballots are sorted. Those bins correspond to 1) ballots that had no problem being scanned, 2) ballots with write-ins and 3) ballots that require poll workers to resolve problems (such as check marks where there should have been oval fill-ins).
It's unclear if Murtaugh is claiming that 15-20% of the ballots in the "problem" bin were altered, or if he means 15-20% of all ballots were altered or "cured".
So my initial question with regard to mechanics of recount is: Are these "problem" ballots segregated from the entire pool of ballots, or are they physically mixed with all "non-problem" ballots?