http://iscoresports.com/

In our Little League, we have both an official scorekeeper and official pitch counter. When there is a discrepancy between two counts (checked after each inning), the pitch counter's numbers are used. How do I adjust the total pitches for a pitcher in iScore after an inning has completed (on those times where the counter has a different number)?

You would have to enter pitches. iScore calculates pitch counts based on the pitches you have actually entered for a pitcher. You can not just manually change those counts.