Unique ballot numbering is the primary way to account for all ballots, to ensure that no extra ballots were inserted, and that no duplicates are present. The numbering requirement helps to make sure that the ballots (or Cast Vote Records) are the real ones. Without unique identifiers for each ballot there is no way to know whether the electronic ballots counted in a recount are faked.
https://blackboxvoting.org/the-case-of-dr-laura-pressley/