​Hi Reza,

Yes, if two crystals of your molecules are isomorphous then it is reasonable to guess that both the phases and the amplitudes for the two crystals are similar.  In such a case, as a first approximation to the structure factors for either crystal, you could take the amplitudes from one and the phases for the other. You could also average phases or amplitudes from the two crystals.  In all these cases you would want to be aware that you are using information from different crystals at this stage in structure determination and therefore that the maps that you would get would have mixed information about the two crystals.

All the best,

Tom T