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In a group I currently run, there is an Aarakocra ranger that likes to fly a lot. It's been fun overcoming some of the challenges this can bring to the table, but I have something coming up that I'm not sure how to handle.

The group are about to spend a few sessions wandering through a big ol' forest, one of the ranger's favoured terrains.

Would their bonuses still apply to the party if the ranger is scouting ahead flying above the tree tops?

They aren't strictly with the party, or even really 'in' the terrain. Does the ranger have to travel on foot with the party for them to take advantage of the natural explorers bonuses? Would only some of the bonuses count?

The ranger benefits still apply.

Good question! A ranger's Natural Explorer feature is not an aura spell, but instead comes from their knowledge of the terrain. While certain skill checks would have problems with flight (being stealthy while out in the middle of the sky, for example), the benefits of Natural Explorer wouldn't be affected in any special way. Let's look at the benefits of Natural Explorer from an RP perspective:

• 
  Your group can’t become lost except by magical means. The ranger is flying and quite literally has the bird's eye view. He's not going to let the group get lost.


• 
  Even when you are engaged in another activity while traveling (such as foraging, navigating, or tracking), you remain alert to danger. This wouldn't change at all, since he's still looking for danger up in the air. You might make his perception check at disadvantage for ground-based enemies due to canopy cover and distance, but that's a limitation on perception checks in general while flying.


• 
  If you are traveling alone, you can move stealthily at a normal pace. There's not really any place to conceal yourself while flying, but that's more a limitation of stealth in general. If he finds a way to be stealthy in the air, he would move at a normal pace.


• 
  When you forage, you find twice as much food as you normally would. There's nothing about foraging that would be limited by flying. You might get more duck meat than boar meat, but nothing mechanical should change.


• 
  While tracking other creatures, you also learn their exact number, their sizes, and how long ago they passed through the area. This would probably require the ranger to examine the tracks more closely, but that's a limitation on the tracking survival checks in general.


• 
  Difficult terrain doesn’t slow your group’s travel. As a ranger, it's generally assumed you would set the path and warn your group about techniques for navigating your favored terrain. This is one of those situations that don't need to be explicitly played out. And you said yourself, the ranger is scouting ahead. Any exceptionally difficult terrain would be spotted and reported back.

Honestly, the ranger is doing exactly what a ranger would be doing, taking the lead and keeping an eye out for any upcoming problems. Flight has it's own challenges from a role playing perspective, but that shouldn't affect the ranger's ability in any special way.