Integrating the design and creation of fault identification and diagnostic capabilities into Model-Driven Development methodologies is one approach to enhancing the resilience of Industrial Cyber-Physical Systems. We present a Fault Diagnostic Engine designed to recognise and diagnose faults in IEC 61499 Function Block Applications. Using diagnostic agents that interact directly with the target application, we demonstrate fault monitoring and analysis techniques and as well as failure scenario intervention. By designing and building fault diagnostic resources during early phases of Model-Driven Development, both iterative testing and long-term fault management capabilities can be created. While applying and refining appropriate model artifacts, we demonstrate that the concurrent development of function blocks alongside fault management capabilities is both feasible and worthwhile.