The paper deals with reconfigurable software component-based embedded control systems. We define a Control Component as a software unit to support control tasks of the system which is assumed to be a network of components with precedence constraints. We define an agent-based architecture to handle automatic reconfigurations under well-defined conditions by creating, deleting or updating components to bring the whole system into safe and optimal behaviors. We model the agent by nested state machines where states correspond to other state machines in order to cover all reconfiguration forms. Several complex networks can implement the system where each one is executed at a given time when a corresponding reconfiguration scenario is automatically applied by the agent. To check the correctness of each one of them, we apply in several steps a refinement-based approach that automatically specifies feasible Control Components according to the formalism Net Condition/ Event Systems (abbr. NCES) which is an extension of Petri nets. The model checker SESA is automatically applied in each step to verify deadlock properties of new generated components, and it is manually used to verify CTL-based properties according to user requirements. Two Industrial Benchmark Production Systems FESTO and EnAS available in our research laboratory are applied to explain the paper contribution.