From what I remember reading they will take both scores and mark the second credit as a duplicate credit but take the higher score when they figure your EC GPA. You have a second GPA that will reflect any cources you earned credit in and all credits will show up on your transcript. The only grades you "get rid of" are classes you attempted before enrolling in which your transcripts shows a "W, F, I" or otherwise shows no credit awarded.

At least that is what I gathered from the handbook. Check with your advisor when you apply.