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When you add a flight-duty (CDR Definition - type other, on acft) in the section Crew > Duties, you can now select an option 'CPT or FO (best). It means, that if a pilot has both CPT & FO ratings and he is added to flight-duty as 1st - Leon will pick the highest rating (CPT). If CPT function has already been assigned to other pilot - such a pilot will be automatically assigned as FO.