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Digital technology for 3D survey and virtual modeling of historical buildings has been largely improved in the last years. However, virtual reconstructions of lost buildings still offer hermetic interpretations, so that it is almost impossible to understand them critically. Such models usually avoid the diachronic perspective that is closely related to the evolutionary and complex essence of historical constructions. The present paper addresses the innovative case study of the Early Medieval monastic church of San Cebrián de Mazote (Valladolid, Spain), which has been analised to know the original building and its later additions and restorations. Besides that, this paper proposes theoretical guidelines to develop current digital 3D models of historical buildings into advanced ones by means of implementing their transformation sequence and complex essence (metadata), as well as the interpretation process that has been taken during the research (paradata). [ABSTRACT FROM AUTHOR]