In minimally invasive surgical robotics, catheter-scale Fiber Bragg Grating (FBG) sensors are promising due to their ability to estimate multi-dimensional forces by multiplexing several optical channels. However, deploying these compact multi-channel sensors introduces two critical engineering challenges: inherent nonlinear cross-axis coupling during complex deformations, and intermittent channel dropouts caused by fiber fractures in constrained workspaces. These compounding issues severely degrade force estimation. Existing fault-tolerant approaches rely on combinatorial model banks, which scale exponentially with the channel count and demand prohibitively expensive per-pattern calibration. In this paper, we propose a unified, self-supervised mask-aware Transformer that explicitly models channel availability to enable graceful degradation under diverse and dynamic sensor failures. The encoder is pretrained via masked-channel reconstruction on unlabeled data streams and fine-tuned for force regression using a balanced clean-and-corrupted-view objective alongside a dynamic corruption curriculum. Furthermore, a parallel uncertainty head, trained via heteroscedastic Gaussian negative log-likelihood, predicts per-axis confidence in a single forward pass, circumventing the overhead of multi-pass ensembles. Evaluated on a catheter-scale 8-channel FBG dataset, our single unified model achieves a nominal Root Mean Square Error (RMSE) of 0.0066~N and degrades gracefully to 0.0126~N under severe 4-channel failures. This significantly outperforms a comprehensive model bank of 255 per-pattern neural networks (0.0154~N at 4-channel loss) while eliminating pattern-specific calibration.

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