Modular systems offer increased system versatility and efficiency. Work-drive systems are a subset of mechatronic systems, often modular, featuring a working function and a driving function. Efficient module changes are a core challenge of modularity as software adaptations are needed to accommodate the various module functionalities, geometries and dynamics. Traditional virtual commissioning reduces the development time of products and systems. Additionally, quality improvements are achieved by virtue of earlier and more thorough testing in a risk-free environment. Specifically, control software developed and tuned using a system’s virtual replica can be deployed to the system with little or no modifications. Current virtual commissioning solutions lack automated capabilities or solely employ kinematic models. The digital twin framework proposed in this paper for automated virtual re-commissioning uses a dynamic multibody model to adapt software during module changes in an operating environment with little to no help from a human operator. The proposed framework is demonstrated in simulation for low-level control loop re-commissioning. A sample task sequence is executed in three test cases: 1) baseline 2) system parameter change 3) low-level controller re-tune. The simulation results show an increase in tracking error in 2) compared to 1), illustrating the need for controller re-tune. This subsequently brings back similar performance as the baseline case, i.e. a decrease of 10% tracking error in 3) compared to 2).