The growing use of 3D technologies in the cultural heritage sector has raised important questions about striking the right balance between making information accessible for dissemination and ensuring its reliability for documentation purposes. Although digital models are now routinely produced and published across museums and research institutions, their processing often involves undocumented interventions, particularly when addressing missing or incomplete data arising from acquisition constraints. This lack of transparency could undermine the scientific value of 3D assets and limit their reusability. This paper presents a methodological pipeline, developed within the CHANGES project (Spoke 4: Virtual Technologies for Museums and Art Collections), which aims to align 3D digitisation practices with the FAIR principles of findability, accessibility, interoperability and reusability. The pipeline was tested on the large-scale digitisation of over 380 objects from the Aldrovandi exhibition and the Giovanni Capellini Geological Museum at the University of Bologna. It introduces a structured workflow that preserves and documents each version of the 3D model derived from the raw acquisition data. To address the aforementioned critical issue of transparency, the Vertex Colour Map methodology is proposed, which visualises operator interventions directly on the geometry. By embedding paradata in the geometry of the 3D model as a semantic layer, this approach enables users to distinguish between regions acquired faithfully and portions that have been reconstructed, thereby ensuring an informed interpretation of the model. Three case studies demonstrate the effectiveness of this method in documenting uncertainty and enhancing accountability in the modelling process. The results show that incorporating systematic paradata visualisation within FAIR-aligned workflows establishes a sustainable framework for the 3D digitisation of Cultural Heritage, enabling models to be used as tools for dissemination, research and long-term preservation simultaneously.