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In today's globalized markets the manufacturing industry in traditional high-wage countries highly depends on flexible and automated manufacturing systems to remain competitive. State-of-the-art industrial control and automation systems do not sufficiently solve the problem of downtimeless reconfiguration of control applications. This paper presents an approach for structured modeling of controlled reconfigurations of control applications based on IEC 61499. The reconfiguration process itself with this paper defined as evolution allows close interaction with applications or physical processes while modeling knowledge from control engineering is reused for evolution engineering. An example points out the evolution engineering process as well as the benefits of this new approach.