One of the main problems of modern manufacturing systems is the increasing complexity related to modern Industry 4.0 technologies that are fundamentally changing manufacturing and logistics processes and operations. Industry 4.0 includes, e.g., flexible automation and robotization, which make complex manufacturing systems difficult to analyze. Some modeling and simulation methods are being used to solve industrial problems and can serve as an interface between the production level and management level. The new trend of the Digital Twin, creating simulation models as similar as possible to the real system, and a Digital Twin framework for a manufacturing line from the automotive industry, was considered. Simulation models typically start from the empty state and some warmup time is required to achieve the stable state. The Key Performance Indicators were also analyzed for the stable state. However, there are many stochastic parameters such as machinery failures, human errors, quality issues, etc., that make the real processes differ from simulated processes, and cause the instability of production throughput and changes in the Work in Process. To analyze the Work in Process in the model, initialization of the model with proper production data is required, as the Digital Twin uses data synchronization with the production database. In this paper, the digital model of a human-robot-operated manufacturing system with Work-in-Process data synchronization is analyzed, and the results of the statistical analysis of simulation experiments are presented. The obtained results show high variability of finished production, which is related to system instability due to random failures, especially when the system starts from an empty state. However, an increase in initial Work in Process results in better efficiency and stability for the whole system. The DT simulation of the manufacturing system can be very helpful, as it becomes a repository of knowledge about the real system and enables the analysis of its dynamics. However, for proper functionality, the model should include information about the current WIP state, which enables the start of the simulation with exactly the same number of queues as in the real system. The presented method can also be used in similar enterprises from other industries, especially for those with discrete processes or high WIP variability, and for further synchronization of other DT parameters.