Inaccurate representation of atmospheric processes by transport models is a dominant source of uncertainty in inverse analyses and can lead to large discrepancies in the retrieved flux estimates. We investigate the impact of uncertainties in vertical transport as simulated by atmospheric transport models on fluxes retrieved using vertical profiles from aircraft as an observational constraint. Our numerical experiments are based on synthetic data with realistic spatial and temporal sampling of aircraft measurements. The impact of such uncertainties on the flux retrieved using the ground-based network and those retrieved using the aircraft profiles are compared. We find that the posterior flux retrieved using aircraft profiles is less susceptible to errors in boundary layer height, compared to the ground-based network. This finding highlights a benefit of utilizing atmospheric observations made onboard aircraft over surface measurements for flux estimation using inverse methods. We further use synthetic vertical profiles of CO₂ in an inversion to estimate the potential of these measurements, which will be made available through the IAGOS (In-service Aircraft for a Global Observing System) project in the future, in constraining the regional carbon budget. Our results show that the regions of tropical Africa and temperate Eurasia, that are under-constrained by the existing surface-based network, will benefit the most from these measurements, with a reduction of posterior flux uncertainty of about 7 to 10 %.