Network digital twin (NDT) models are virtual models that replicate the behavior of physical communication networks and are considered a key technology component to enable novel features and capabilities in future 6G networks. In this work, we focus on communication-aware control applications and study NDTs that model the communication quality properties of a multi-cell, dynamically changing wireless network over a workspace populated with multiple moving users. We propose an NDT modeled as a hybrid system, where each mode corresponds to a different base station and comprises sub-modes that correspond to areas of the workspace with similar network characteristics. The proposed hybrid NDT is identified and continuously improved through an annealing optimization-based learning algorithm, driven by online data measurements collected by the users. The advantages of the proposed hybrid NDT are studied with respect to memory and computational efficiency, data consumption, and the ability to timely adapt to network changes. Finally, we validate the proposed methodology on real experimental data collected from a two-cell 5G testbed.