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During the past years, it has been shown that dynamic reconfiguration of FPGAs can be used to enhance the resource efficiency and flexibility of digital controllers. The authors have developed a system architecture, which allows the reconfiguration of FPGA-implemented controllers during runtime. Depending on the operating regions of the controlled plant different controllers can be dynamically loaded into the system. In this paper we present a design flow that enables an automated generation of such partial controllers. Furthermore, a high-level design entry allows a comfortable simulation of the controllers with sophisticated tools such as Matlab Simulink.