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This paper deals with distributed multi-agent reconfigurable embedded control systems following the International Industrial Standard IEC 61499 in which a Function Block (FB) is an event-triggered software component owning data and a control application is a network of distributed blocks that should satisfy functional and temporal properties according to user requirements. We define an architecture of reconfigurable multi-agent systems in which a Reconfiguration Agent is affected to each device of the execution environment to apply local reconfigurations, and a Coordination Agent is proposed for coordinations between devices in order to guarantee safe and adequate distributed reconfigurations. A communication protocol is proposed to handle coordinations between agents by using well-defined Coordination Matrices. We specify both reconfiguration agents to be modeled by nested state machines, and the Coordination Agent according to the formalism Net Condition-Event Systems (NCES) which is an extension of Petri nets. To validate the whole architecture, we check by applying the model checker SESA in each device functional and temporal properties to be described according to the temporal logic “Computation Tree Logic.” We have also to check all possible coordinations between devices by verifying that whenever a reconfiguration is applied in a device, the Coordination Agent and other concerned devices react as described in user requirements. The paper's contributions are applied to two Benchmark Production Systems available in our research laboratory.