We present a scalable approach to automatically re-configure evolving IEC 61499 systems for deployment onto an available set of resources. We capture system architecture and high-level configuration requirements formally, and use an efficient SMT-based constraint resolution to generate a valid system configuration. Any changes in the system architecture, configuration requirements, or resources are automatically translated into a minimal set of updated constraints, allowing a faster reconfiguration as compared to a monolithic approach where the whole system is re-configured. We show the feasibility of our approach by studying an airport baggage handling system developed using the IEC 61499 standard.