For bilayer stacks of non-centrosymmetrical molecules, formed by the Langmuir-Blodgett (LB) technique (Y deposition), 00l peaks for the bilayer period are usually observed in the X-ray specular reflectivity curve. In this study, we show that the introduction of stacking disorder at lower transfer ratios and the subsequent partial repair of defects by a parallel shift of oppositely oriented molecules into the vacancies may result in the formation of antiphase domains and in an increase in the average monolayer symmetry followed by quenching of the bilayer peaks. The X-ray reflectivity data, obtained for multilayers of penta-alkynes, are used to demonstrate this real structural effect, which is expected to be of general importance for X-ray and neutron reflectivity data reduction and for the structural modelling of multilayers.