Unless you specifically want a Learner's overall Course Status to show an entirely different state from those provided in the Course's individual Lessons, it is strongly recommended that you make sure that you duplicate your changes from one area to the next, so that both results match.
This recommended practice holds true for Statuses, as well as for how Scores are determined, because both of these items allow for separate values to exist across the Course Activity and Lesson Activity levels in the LMS.
It is true that sometimes you might need to manually override a Course Status, in order to be able to carry something out, but you still might want to hold onto the underlying Lesson Activity data that the LMS used to generate the Learner's original Course Activity entry. For situations like this, having different information may be exactly what you want.
Otherwise, minimize any future confusion in your Course Activity Report and make it a habit of making sure that things match.