The historical "Operation Northwoods" plot is viewed by many as a paradigmatic blueprint for the 9/11 attacks: the original four planes were replaced by drones and landed at secret locations while the drones were directed into their respective targets. It is possible to reconstruct the flight route of a plane by its radar data, but radio records from air traffic control and ACARS messages are fundamental tools for this purpose, too. Needless to say, these three data sets should coincide 100% in order to exclude a plane swap scenario à la Operation Northwoods. But they don't. For example, controllers were tracking Flight 11 still after the North Tower crash, so we have a contradiction between ATC radio talks and the RADES radar data. And then there's ACARS.
http://911woodybox.blogspot.de/2012/10/united-93-received-18-acars-uplinks.html