Hi Naildgmat,
I was an admissions assistant when I was an MBA student at the University of Chicago (now Booth). My instructions were always clear..."take the highest score." I feel that there are two major items you can share with your friend that will put her at ease.
The first is that the GMAT score is conveying a level of preparation and readiness for getting an MBA. Test takers do not luck into a good score, they earn it. The people looking at her business school application with see both test scores and see that she recognized a weakness (a low GMAT score) and addressed it with preparation. This is a regular occurrence and does not reflect negatively upon the applicant. When I was looking at applications, I recall that about 50% of them had more than one GMAT score.
The second item is based on my instructor experience. When I have worked with GMAT students who have applied to business school but not been accepted, the reason they are often working with me is because the students have been given feedback from admissions that they need to improve their GMAT score. Maybe not as important but still of note I think is that it is in the school's best interest to look at the highest score. One of the common parameters for B-school rankings is the average GMAT score of the admitted/incoming students. I think this further reinforces that the schools are interested in the highest score, not the first.
I hope this puts your friend's mind at ease!
Keith