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Cyber-physical systems often contend with incomplete architectural documentation or outdated information resulting from legacy technologies, knowledge management gaps, and the complexity of integrating diverse subsystems over extended operational lifecycles. This architectural incompleteness impedes reliable security assessment, as inaccurate or missing architectural knowledge limits the identification of system dependencies, attack surfaces, and risk propagation pathways. To address this foundational challenge, this paper introduces ASTRAL (Architecture-Centric Security Threat Risk Assessment using LLMs), an architecture-centric security assessment technique implemented in a prototype tool powered by multimodal LLMs. The proposed approach assists practitioners in reconstructing and analysing CPS architectures when documentation is fragmented or absent. By leveraging prompt chaining, few-shot learning, and architectural reasoning, ASTRAL extracts and synthesises system representations from disparate data sources. By integrating LLM reasoning with architectural modelling, our approach supports adaptive threat identification and quantitative risk estimation for cyber-physical systems. We evaluated the approach through an ablation study across multiple CPS case studies and an expert evaluation involving 14 experienced cybersecurity practitioners. Practitioner feedback suggests that ASTRAL is useful and reliable for supporting architecture-centric security assessment. Overall, the results indicate that the approach can support more informed cyber risk management decisions.