Near-IR observations of protoplanetary disks provide information about the properties of the inner disk. High resolution spectra of abundant molecules such as CO can be used to determine the disk structure in the warm inner parts. The $v2/v1$ ro-vibrational ratio of $v_{1-0}$ and $v_{2-1}$ transitions has been recently observed to follow distinct trends with the CO emitting radius, in a sample of TTauri and Herbig disks; these trends have been empirically interpreted as due to inner disk depletion from gas and dust. In this work we use existing thermo-chemical disk models to explore the interpretation of these observed trends in ro-vibrational CO emission. We use the radiation thermo-chemical code ProDiMo, exploring a set of previously published models with different disk properties and varying one parameter at a time: the inner radius, the dust-to-gas mass ratio, the gas mass. In addition, we use models where we change the surface density power law index, and employ a larger set of CO ro-vibrational levels, including also fluorescence from the first electronic state. We investigate these models for both TTauri and Herbig star disks. Finally, we include a set of DIANA models for individual TTauri and Herbig disks which were constructed to reproduce a large set of multi-wavelength observations.