A method of operating a printer includes operating an actuator with a controller to move a printhead array during a print job. The controller operates a first subset of inkjets in the printhead array to print to a first print medium during the job and moves a first inkjet in the printhead array over a second print medium while removing a second inkjet that was over the first print medium from being over the second print medium. The controller uses the inkjets that are over the second print medium, including the first inkjet but not the second inkjet, to form a printed image on the second print medium.