The CoVHer Erasmus+ project addresses the long-standing lack of standardisation in hypothetical virtual 3D reconstruction and modelling in architectural heritage research. It aims to develop best practices for the 3D reconstruction of lost or never-built architectural heritage, enhancing research quality, transparency, and reusability. The collaborative effort includes contributions from five European universities and two private companies, focusing on architecture, archaeology, digital humanities, and art history. The presented workflow of documentation is the result of the joint effort in extensions of the approaches of the Scientific Reference Model (SRM) and Critical Digital Model (CDM), which strive for faithful reconstruction, documenting all decisions and inferences and advocate open licensing and use of non-proprietary formats to promote accessibility and reusability. The developed methodology aims to provide tools for the scientific evaluation of hypothetical reconstructions and support data exchange between researchers.