This is what it says under the section labelled "4.1 Presidential Race" in the Cyber Ninjas Report, Vol. III.

The chart below summarizes the results of the hand-recount of the Presidential Race of the Maricopa County Forensic Audit. These tallies are based on the tallies from all original ballots and does not include the ballots duplicated from the originals.

However, under "5.2 Finding Summary Table" there's a list of the various kinds of illegitimate ballots that they found, most of which were not duplicates, and therefore would've still been included in the hand recount.