I think you are looking for:
$query="UPDATE `FlightSchedule` SET delay = CEIL((UNIX_TIMESTAMP(time1) - UNIX_TIMESTAMP(time2))/60) WHERE `flightNum_arr`='".$flightNum_arr."';";
As an alternative, there is a TIME_TO_SEC function - and since it gives a result in seconds, you also need to divide it by 60.
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