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So recently, I got a D on AP English Language first semester but I am making it up during summer school, but the summer class is only regular English. I know however that I am going to get an A. Will colleges such like the UCs be able to see the D I got or just the grade that was made up?

They will see both grades.

They will see both grades - and because it isn’t the exact same course, the D will probably be in your GPA (with no AP bonus pt)