Graphene is an ideal material for biosensors due to the large surface area for multiple bonding sites, the high electrical conductivity allowing for high sensitivity, and the high tensile strength providing durability in fabricated sensor devices. For graphene to be successful as a biosensing platform, selectivity must be achieved through functionalization with specific chemical groups. However, the device performance and sensor sensitivity must still be maintained after functionalization, which can be challenging. We compare phenyl amine and 1,5-diaminonaphthalene functionalization methods for chemical vapor deposition grown graphene, both used to obtain graphene modified with amine groups-which is required for surface attachment of highly selective antibody bio-receptors. Through atomic force microscopy (AFM), Raman spectroscopy, and time-of-flight secondary ion mass spectrometry imaging of co-located areas, the chemistry, thickness, and coverage of the functional groups bound to the graphene surface have been comprehensively analyzed. We demonstrate the modification of functionalized graphene using AFM, which unexpectedly suggests the removal of covalently bonded functional groups, resulting in a "recovered" graphene structure with reduced disorder, confirmed with Raman spectroscopy. This removal explains the decrease in the ID/IG ratio observed in Raman spectra from other studies on functionalized graphene after mechanical strain or a chemical reaction and reveals the possibility of reverting to the non-functionalized graphene structure. Through this study, preferred functionalization processes are recommended to maintain the performance properties of graphene as a biosensor.