But didn’t the SOS tell the elections folks to not report the vote differences from election day and he only posted the original numbers? I know read something about that.
Yes, he did that. Since the audited count still verified the outcome of the original count, he stuck with the original count. I think the originally uncounted votes in Floyd County and the ballots found somewhere else were added in, but in Counties where there was just a difference, the question arises "which count to report?". It really doesn't make a hill of beans difference in the end. The machines were shown to have reported correctly, and one could argue they were more accurate than human counting.
The bottom line is that two disparate systems for counting the votes were used and the same outcome resulted.