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Real-time supervisory control of advanced reactors requires accurate forecasting of plant-wide thermal-hydraulic states, including locations where physical sensors are unavailable. Meeting this need calls for surrogate models that combine predictive fidelity, millisecond-scale inference, and robustness to partial observability. In this work, we present a physics-informed message-passing Graph Neural Network coupled with a Neural Ordinary Differential Equation (GNN-ODE) to addresses all three requirements simultaneously. We represent the whole system as a directed sensor graph whose edges encode hydraulic connectivity through flow/heat transfer-aware message passing, and we advance the latent dynamics in continuous time via a controlled Neural ODE. A topology-guided missing-node initializer reconstructs uninstrumented states at rollout start; prediction then proceeds fully autoregressively. The GNN-ODE surrogate achieves satisfactory results for the system dynamics prediction. On held-out simulation transients, the surrogate achieves an average MAE of 0.91 K at 60 s and 2.18 K at 300 s for uninstrumented nodes, with $R^2$ up to 0.995 for missing-node state reconstruction. Inference runs at approximately 105 times faster than simulated time on a single GPU, enabling 64-member ensemble rollouts for uncertainty quantification. To assess sim-to-real transfer, we adapt the pretrained surrogate to experimental facility data using layerwise discriminative fine-tuning with only 30 training sequences. The learned flow-dependent heat-transfer scaling recovers a Reynolds-number exponent consistent with established correlations, indicating constitutive learning beyond trajectory fitting. The model tracks a steep power change transient and produces accurate trajectories at uninstrumented locations.