This question actually was answered, Exid. Supplement pg 23 under sweeping. When a flyer makes a sweeping melee attack, the first target will determine whether the attacker loses or retains the flying trait. A nonflying attacker with reach can do a sweeping attack against both flyers and nonflyers. A flying attacker can not. Reach only allows nonflyers to attack flyers, not the other way around.
Thus, if you make a sweeping melee attack with a flying creature who has the reach trait, and your first target is a nonflyer, then you'll lose the flying trait and your second target can be either a flyer or a nonflyer. If your first target is a flyer though, then your second target must also be a flyer because the attacker is still flying.