That assumes they don't mix the "found" ballots in with the ballots that were properly handled during the election. If they do, how can you tell, and how can you unscramble the omelet?
From what I read, a couple of ballot boxes were found in a storage room in a school. Since those ballots are not part of the chain of custody, you don’t count them. The only ballots that count are those that are voted, collected, and delivered to the BOE with the aggregate. None of this “oops...I found this box a day or two later” crap.