A recount isn't the place to check if your voting system is working or not.
If you want to audit the voting system, then you do an audit. Set up a dry run, run through the process, and check the results. Then compare them with the results of a real election, when you aren't time constrained and can do it properly.
There is going to be some margin of error, preferably pretty low. You want them to be the same during the audit than during the election. You don't do the election first then do the audit - it's basic process control theory.
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