In terms of PharmCAS, all classes you've taken will be factored into your cumulative GPA. They also break it out in more detail - like math GPA, science GPA, etc. - and each of these sections include all of the classes you've taken.
However, many schools calculate their own GPA for you, and those formulas are individual to each school. Some schools honor academic forgiveness; some calculate retakes differently. You would need to research / contact your prospective schools for the best answer.
Honestly, what's your cumulative GPA to this point? How much more do you have to go? (Are you, say, at year 2 of a 4 year program?)
If it makes you feel better, I got an F in Calc III... which isn't even required. Brought my cGPA down ~0.2, and I've taken a lot of classes. 🙄