Digital Twin technology within the AEC industry is a crucial topic for the effective management of the built environment. The PNRR-funded research project Tecnodigit also focuses on this strategy, proposing a more effective integration of sensor data into BIM models to guarantee a higher level of building safety and sustainability. Among the case studies involved in the research project, the underground facilities of National Gran Sasso Laboratories represent an exceptional example not only for their unusual location, but also for their unconventional building typology mixing buildings and infrastructural features. The challenge of developing a federated BIM model of the central tunnel containing the experiments within for physics particles involves the overcoming of several criticalities that are described and highlighted in the paper, along with the proposal of possible solutions that represent the first phases for the application of a DT system.