Digital and simulation models support the design and management of complex systems. However, system modelling is a time-demanding and knowledge-intensive activity. Moreover, modern manufacturing systems are subjected to frequent changes in production plans and subsequent reconfigurations. Therefore, the quick regeneration of the digital models is necessary to align digital twins and cyber-physical systems. This paper proposes a novel event-centric process mining paradigm, a process discovery algorithm, and a set of Key Performance Indicators for the fast and automated generation of digital models and their benchmarking. The discovery algorithm is based on the Event Relationship Graph of the conceptual model of the physical line. The algorithm is tested in four realistic systems of increasing complexity to verify the accuracy in modelling multi-product systems with re-entrant flows and random reworks in the presence of the assembly, disassembly, and split processes beyond the processing operations, and multi-operation workstations. The Event Relationship Graphs of the four systems are presented through the equivalent Petri nets models. The proposed approach is suitable for systems where the sensor positions are known and meaningful, like manufacturing systems, and it is effective for the quick automated generation of digital models for the activities of production planning and control as it requires a few seconds of computation time and a few hours of system observation.