They used to have several such "combined" flights with the same flight number when Aegean started flying. For example, HER-ATH-FCO or RHO-ATH-XXX. Back then (i.e., very early '00s), these counted as a single flight (segment). These one-flight-number flights with an intermediate stop in ATH (and SKG?) no longer exist in the A3 network, but they do in the OA one. My (un)educated guess is that they still count as a single segment, but I may well be wrong.