Industrial Control Systems (ICSs) are widely used in various industries, enabling the control and monitoring of critical infrastructures such as microgrids. In these infrastructures, distributed and cooperative control systems are commonly employed to synchronize set points through information exchange over communication networks. However, these systems are increasingly vulnerable to various security threats, particularly those targeting synchronization data. This paper proposes a network reconfiguration mechanism leveraging Software-Defined Networking (SDN) to mitigate synchronization attacks in distributed and cooperative microgrid control systems. We implement and evaluate our proposed mitigation algorithm using MiniCPS to show its efficacy in avoiding synchronization attacks within such distributed energy systems.