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Reconfiguration is an important feature for industrial automation systems to provide flexibility, adaptability, and resilience. Dynamic reconfiguration of real-time systems requires both functional and temporal correctness. A lengthy disruption of real-time behaviors caused by a reconfiguration can cause the system to fail. We describe the scheduling problem for a component-based real-time industrial control system on the basis of the IEC 61499 and extend this problem to handle disruptions introduced by a dynamic reconfiguration. We show that the disruption can be quantified by applying the Priority Ceiling Protocol (PCP) and calculating the blocking time. Further, we show that the order of operations within a reconfiguration sequence can be optimized using the blocking time as objective function. An evaluation on two example systems shows that our model allows the application of common schedulability tests for …