See you are still concerned with which candidate won which ballot. The easier thing to do is to count the total number of ballots physically, initially. Should the physical count be off from the reported count then do a physical recount of ballots.
Everyone keeps saying that digital is easy to track. However as a DB Analyst, this is furthest from the truth. Digital breadcrumbs can be and have been manipulated before. They could be erased with a simple script that would have no footprint at all. As an example, system dates can be changed to produce a faulty date then all footprints in the system would not be in question as far as dates go. Many ways to get around the writing of a footprint in order to mke it look on the up and up.
I think the concern is how do you isolate bad ballots(having come in after the deadline dates) from good ballots when they are all mixed together when all other numbers match. You can’t but if the numbers are enough that can significantly throw an election then the whole batch has to be disqualified.
Physical ballots and their counts must match the data tape/file/numbers. If they don’t then there was a programming issue with the tabulators. Physical ballot numbers must match the polling logs of the precincts of those registered voters of the precinct who are recorded as having voted that particular election. There will be some who may not have voted. Any number over 90 percent starts to look suspicious and anything over 100 percent not supported by same day registration additions shows over voting.