I suspect your daughter has misbehaving Eustachian tube and retraction/fluid in the middle ear. I agree that giving her more antibiotics is not likely to help this, but disagree that 2 courses of antibiotics has "devastating effects" on the bacterial flora and is now somehow the cause of her "flaring infections". Taking antibiotics will likely alter the make-up of the intestinal flora, but this most often goes unnoticed by the individual, changes once the treatment is stopped (we eat bacteria every day) and has not be shown to cause infections on a wide scale (there are some who can have problems when one type of bacteria is allowed to overgrow).
Patients with the symptoms your daughter describes often have middle ear fluid, but this is not necessarily infected fluid -- and I doubt your daughter still has an "infection" in her ear. Regardless, if it causing this degree of trouble, there are things an ENT doc can do to help her. And yes, changes in altitude would only be making this worse for her.
Did they say anything about the pressure inside the ear?
Two treatments of antibiotics has devastating effect on the bacterial flora in the intestines and could very well be the cause of flaring infections (i speak from experience).