X-ray computed tomography is a powerful tool for volumetric imaging, but requires the collection of a large number of low-noise projection images, which is often too time consuming, limiting its applicability. In our previous work \cite{shang2023stereo}, we proposed a stereo X-ray tomography system to map the 3D position of fiducial markers using only two projections of a static volume. In dynamic imaging settings, where objects undergo deformations during imaging, this static method can be extended by utilizing additional temporal information. We thus extend the method to track the deformation of fiducial markers in 3D space, where we use knowledge of the initial object shape as prior information, improving the prediction of the evolution of its deformed state over time. In particular, knowledge of the initial object's stereo projections is shown to improve the method's robustness to noise when detecting fiducial marker locations in the projections of the deformed objects. Furthermore, after feature detection, by using the features' initial 3D position information in the undeformed object, we can also demonstrate improvements in the 3D mapping of the deformed features. Using a range of deformed 3D objects, this new approach is shown to be able to track fiducial markers in noisy stereo tomography images with subpixel accuracy.