A continuous web printer that has an inlet for receiving a web of media from a media web roll unwinder, an outlet for delivery to a media web roll winder, a media feed path extending from the inlet to the outlet, a plurality of pagewidth inkjet printhead assemblies positioned adjacent the media feed path for printing on both sides of the web and a central processor for inputting print data to the pagewidth inkjet printhead assemblies such that during a print run, the pagewidth inkjet printhead assemblies print many copies of a document The central processor is configured to selectively alter one or more of the copies to be non-identical to the remainder of the copies without interruption to the print run.