We theoretically investigate the phonon propagation and thermal conductivity κ in hybrid boron nitride and graphene sheets. By using a real-space Kubo-computational transport scheme, large and disordered graphene structures are simulated, introducing disk-shaped domains with varying sizes of 2 to 8 nm and concentrations ranging from 0% to 100%. A strong influence of the domain size and concentration on the transport properties is obtained. The mean free paths are minimized at 50% domain concentration, and stronger suppression of κ is achieved with smaller domains. It is found to decrease by up to 65% at room temperature when the domain size is 2 nm. These results are beyond the scope of any effective medium approximation.