Embedded systems in robotics or mechatronics need flexibility since they are working in dynamic environments. We consider an embedded modular multi-microcontroller system. Each module includes a microcontroller and special purpose hardware like a motor driver. Usually a change of the embedded software necessitates a direct access to all the devices (microcontrollers) to reload the code. To overcome this disadvantage we introduce an infrastructure for flexible runtime reconfiguration of microcontroller modules within a system. The infrastructure enables the system to be coarse-grain reconfigurable on module level from one single point of access. By using our infrastructure the system can remain operational during reconfiguration except the modules that actually get reconfigured. The infrastructure can cope with hardware changes during runtime like disconnection and reconnection of system parts.