Rust is a sign of deterioration of a metal roof. There are several ways to repair the rusting of a metal roof. First, an evaluation of the overall roof through an inspection to determine how to address the problem. The cause of the roof is of first concern. The integrity of the membrane itself of the underlying structure needs to be evaluated. Other factors include laps, penetrations, drainage, sky panels, and fasteners. There are several maintenance methods that can be used to address rust, but only an evaluation from a commercial roofing expert can give you the best options.