We are conducting a multi-wavelength analysis of high-resolution molecular spectra that probe the evolution of gas in the inner 10 au in protoplanetary disks. A sample of 15 disks has been combined to probe a range of inner disk structures including small and large dust cavities. Half of the sample has been observed in far-ultraviolet H2 emission with a new HST-COS program (GO-14703), that we have combined to near-infrared spectra of CO emission as observed with VLT-CRIRES and IRTF-iSHELL. This synergic dataset traces the evolution and depletion of CO and H2 in inner disk cavities and shows an evolving radial stratification of the molecular gas, where CO lines are narrower than H2 lines in disks with cavities. CO rotation diagrams also show significant evolution, suggesting a change in gas excitation as CO emission recedes to larger disk radii.