The late-arriving ballots were both physically segregated, and counted separately from the timely ballots by separate government employees, in pairs including one Democrat and one Republican. Before numbers are reported, the numbers in each batch are confirmed by employees locally and at the state level to make sure they match the number of ballots in that batch, and these numbers are reviewed by Democratic and Republican employees.
Segregated numbers have not been reported in this manner because the courts ordered them not to, so the numbers are kept separately and were not included in the official count. Because of the court order, most of the segregated ballots have not yet been counted.
https://www.washingtonpost.com/politics/pennsylvania-ballots... (noting that Alito's order had no effect because that was what the ballot officials were already doing as a result of earlier state court orders.)