It would be very unusual for a harpy eagle to encounter a bald eagle. However, if it was very much determined to, the harpy eagle could use its powerful talons to crush the bald eagle's neck, killing it. This could happen regardless of being in the air or not.
No one knows how much a bald eagles flies in a year. Flying takes a lot of energy in a bird as large as a bald eagle. Therefore, most sensible eagles roost in a tree that gives them a good view of the surround landscape. Only if they spot a potential prey will the eagle take to the wing.