I re-took a class or two, in my freshman year several years before I ever even considered becoming a doctor someday. In my case, the admissions committee noted both old and new grades - they will probably you what happened if you failed a course, they did ask me. I found the admissions committee understanding if you show that you made significant improvement and honestly own up to mistakes and what you learned from them.
Your cumulative GPA is what your university says it is - usually that figures in every class you earned a grade in, averaging all of the grades. For science GPA, you would average all your science grades, re-takes or not. At least, that's how it worked for me. I don't think most universities erase grades of classes you re-take any more.