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In regards of the OpenCV Stitching Pipeline, it's fairly easy:
Deactivate the (homography-based) Rotation Estimator, which would overwrite the existing extrinsic parameters.
Then, use bundle adjustment (ray-based or reprojection-based) to refine the extrinsic and intrinsic parameters.
The documentation is somewhat difficult to understand without background knowledge. I can suggest "Computer Vision: Algorithms and Applications" from "Richard Szeliski" as a read here.
