Micrometer-sized oxidation patterns containing varying composition of functional groups including epoxy, ether, hydroxyl, carbonyl, carboxyl, were created in chemical vapor deposition grown graphene through scanning probe lithography and pulsed laser two-photon oxidation. The oxidized graphene films were then reduced by a focused x-ray beam. Through in-situ x-ray photoelectron spectroscopy measurement, we found that the path to complete reduction depends critically on the total oxygen coverage and concentration of epoxy and ether groups. Over the threshold concentrations, a complex reduction-oxidation process involving conversion of functional groups of lower binding energy to higher binding energy is observed. The experimental observation is discussed and compared to previous work on reduced graphene oxide.