IEC 61499 is a reference architecture for constructing Industrial Cyber-Physical Systems (ICPS). However, current function block development environments only provide limited fault-finding capabilities. There is a need for comprehensive diagnostic tools that help engineers identify faults, both during development and after deployment. This article presents the software architecture for an agent-based fault diagnostic engine that equips agents with domain-knowledge of IEC 61499. The engine encourages a Model-Driven Development with Diagnostics methodology where agents work alongside engineers during iterative cycles of design, development, diagnosis and refinement. Attribute-Driven Design (ADD) was used to propose the architecture to capture fault telemetry directly from the ICPS. A Views and Beyond Software Architecture Document presents the architecture. The Architecturally-Significant Requirement (ASRs) were used to design the views while an Architectural Trade-off Analysis Method (ATAM) evaluated critical parts of the architecture. The agents locate faults during both early-stage development and later provide long-term fault management. The architecture introduces dynamic, low-latency software-in-loop Diagnostic Points (DPs) that operate under the control of an agent to capture fault telemetry. Using sound architectural design approaches and documentation methods, coupled with rigorous evaluation and prototyping, the article demonstrates how quality attributes, risks and architectural trade-offs were identified and mitigated early before the construction of the engine commenced.