Reliable digital recording and analytical interpretation of architecturally complex historic monuments remain challenging, particularly for structures with irregular geometries, stratified construction, and seismic vulnerability. While unmanned aerial vehicle (UAV) photogrammetry, terrestrial laser scanning, and heritage building information modeling (HBIM) have been widely applied in isolation, their integrated use as a coherent, research-driven workflow remains insufficiently explored for Orthodox ecclesiastical museums embedded in dense historic fabrics. To address this gap, we develop and validate a hybrid digital survey methodology combining UAV-based photogrammetry, mobile light detection and ranging, and point-cloud-driven HBIM, applied to the Onufri National Museum in Berat, Albania, a United Nations Educational, Scientific, and Cultural Organization World Heritage context. High-density datasets were processed and converted into a geometrically rigorous HBIM model, enabling the identification of previously undocumented spatial irregularities, dome asymmetries, and constructional hierarchies that are absent from existing archival documentation. The results demonstrate that the proposed workflow achieves sub-centimetric to centrimetric geometric consistency across most elements, significantly improving spatial completeness, modeling reliability, and diagnostic potential compared to conventional survey approaches. Beyond documentation, the HBIM environment functions as an analytical interface for structural interpretation, pathology mapping, and future conservation planning. By foregrounding measurable outcomes and methodological transferability, the study contributes a replicable digital documentation framework applicable to complex heritage buildings in seismic and constrained urban contexts, reinforcing the role of integrated HBIM as a scientific instrument rather than a representational tool in heritage conservation research.