in "The Bourne Legacy" what was Aaron Cross doing in the scene where he had the camera and wires connected to the passport?
He is using High Voltage to de-magnetize a hidden identifying strip in the passport. Since the lack of the presence of this strip doesn't cause any issues at the Airport, we are to assume that her passport had this magnetic identifier because of her job, to keep tabs on her travel. By disabling it, she is able to use the passport and garner no additional attention.
addition He still needed to use her passport as a base to work from, in providing her with credentials to travel with. Using a new picture on the old passport and/or altering the document would be easier than obtaining a new passport.