Rust treatment should be part of a regular roof maintenance program.
If left untreated the rust can destroy a metal roofing system. The rust will create damage to the structural integrity of the metal roof panels. For best practices rust should be treated when it first appears prior to its spreading. It can be important to determine the main cause of the rust. For example: if caused by galvanic corrosion, remove the questionable corrosive metal and replace it with a similar metal to the substrate.
Before applying a rust inhibitor the surface must be thoroughly cleaned to promote proper adhesion. Then the surface must be dried, before applying a surface seal. Then the roof should be treated for rust. Heavy rust may require a second application of rust inhibitor material.