Degradation modeling is essential for failure prognostics of miter gates and subsequent risk-informed maintenance or operational decision-making. Typically, degradation models are formulated based on certain assumptions and simplifications and may not fully capture the complexity of underlying degradation mechanisms. Even minor errors in such models may lead to significant discrepancies in failure prognostics due to error accumulation over time. Aiming to improve the accuracy of the degradation model and ensure reliable failure prognostics, this article proposes a degradation model updating framework for miter gates using normalizing flow-based likelihood-free inference, accounting for both model parameter uncertainty and model form uncertainty (i.e., model bias). The proposed work consists of two phases: the offline training phase and the online updating phase. During the offline training phase, the unknown model bias term is modeled as a random noise with uncertain standard deviation. Synthetic data are then generated using a physical model based on prior knowledge of the uncertain model parameters and model bias. The synthetic data are utilized to train an inference model, which has a summary network for data compression and a conditional invertible neural network for parameter estimation. In the online updating phase, the trained inference model uses strain observations to obtain posterior samples. The Gaussian mixture model and dual particle filter techniques are utilized to recursively update posterior samples, thereby improving the estimation accuracy. Subsequently, model bias is inversely estimated using the degradation model, which uses the updated model parameters and the gap length from the inference model. Following that, a regression model is constructed to correct the biases inherent in the simplified degradation model. This process is implemented iteratively over time to perform continuous model updating and failure prognostics. Results of a case study demonstrate the efficacy of the proposed framework in reducing both model parameter uncertainty and recovering model biases and thereby improving the accuracy of failure prognostics of miter gates.