Ballots themselves do not have unique identifying numbers. But it seems like the data logs from the scanning machines could be used to test whether the same ballots were,scnned nd counted more than once.
1) The time the scanning ballots were recorded should correlate to the time the multi-scanning is shown on the surveillance videos.
2) Stacks of ballots run through the counter multiple times would seem likely to have patterns of votes. Each ballot had multiple offices; these would have specific votes or non-votes for each race. The net ballot in the stack would have it own collection of specific votes and/or omitted votes, and so on. If batches of vote counts in the log repeat these patterns, it will be obvious that the stcks were counted multiple times.
I get the sense that the data analysis to find this was never done. Wonder why... Was Giuliani able to subpoena the digital records? Seems like they are critically important for his defense.
If there is such a file that separates ballots into batches, then any two "batches" with identical vote tallies for every office/measure would almost certainly be double counted. I'm not sure such a file exists for these machines. But I think the extreme circumstances (lying to poll watchers that counting is over for the night, then restarting counting with a smaller group after the poll watchers go home, not to mention pulling hidden ballot boxes from under a table) would 100% require a full recount of all ballots at that facility, under the observation of election lawyers on both sides.
Unfortunately, the professionals (lawyers and poll watchers) of the GOP, think FL 2000, didn't show up. It was amateur hour.