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This paper deals with the dynamic reconfiguration of two manufacturing systems following the component-based International Industrial Standard IEC61499. According to this standard, a function block (abbreviated FB) is an event triggered component owning data and a control application is a FB network that has to meet temporal properties according to user requirements. This FB network is totally changed or modified if a dynamic reconfiguration scenario is applied at run-time. To cover all reconfiguration cases, we classify all possible scenarios in three classes and we define an agent-based architecture designed with nested state machines to automatically handle all possible dynamic reconfigurations.