An understanding of how the convective boundary layer (CBL) is mixed under heterogeneous surface forcing is crucial for the interpretation of area-averaged turbulence measurements. To determine the height and degree to which a complex heterogeneous surface affects the CBL, large-eddy simulations (LES) for two days of the LITFASS-2003 experiment representing two different wind regimes were undertaken. Spatially-lagged correlation analysis revealed the turbulent heat fluxes to be dependent on the prescribed surface flux pattern throughout the entire CBL including the entrainment layer. These findings prompted the question of whether signals induced by surface heterogeneity can be measured by airborne systems. To examine this question, an ensemble of virtual flights was conducted using LES, according to Helipod flight measurements made during LITFASS-2003. The resulting ensemble-averaged heat fluxes indicated a clear dependence on the underlying surface up to the top of the CBL. However, a large scatter between the flux measurements in different ensemble runs was observed, which was the result of insufficient sampling of the largest turbulent eddies. The random and systematic errors based on the integral length scale did not indicate such a large scatter. For the given flight leg lengths, at least 10-15 statistically independent flight measurements were necessary to give a significant estimate of heterogeneity-induced signals in the CBL. The need for ensemble averaging suggests that the observed blending of heterogeneity-induced signals in the CBL can be partly attributed to insufficient averaging.