这样做的时候你是否在乎？

This is a reduced or simplified form. The full form is: If you care when you do [something] In the simplified form, some words are removed. First, the sentence uses a time word ("when," "after," "before," "while") and the subject doesn't change ("you"). In sentences like this, you can remove the second "you" are change the verb to -ing. If you care when you do... = If you care when doing... Second, "do so" refers to an action from an earlier sentence. I don't know the sentence before so I don't know the meaning. But here are some examples. Don't call me at night. If you do so, I'll be mad. (do so = call me at night) It's important to exercise regularly. People who don't do so may have health problems. (do so = exercise regularly)