We extend our method formerly suggested for structure refinement of the amorphous sp2 carbon, based on neutron or x-ray diffraction, and applied to amorphous fullerene and its derivatives produced by vacuum annealing. To diagnose heterogeneous media, the method uses the rigid body molecular dynamics simulations of the domain-like packing for a predefined set of structural blocks. Previously, the sensitivity of the results to the variability of mutual positions of these structural blocks was analyzed in two limiting cases: (A) any domain contains only identical structural blocks and (B) all domains are the identical mixtures of many different structural blocks with variable packing of the blocks. Here, we extend this analysis to intermediate cases which correspond to domains of the type “B” with the subdomains of the type “A”. Such a structuring corresponds to a partial destruction of the nanoscale structure of the sample (e.g. by low-temperature annealing).