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Stokes inversion codes are crucial in returning properties of the solar atmosphere, such as temperature and magnetic field strength. However, the success of such algorithms to return reliable values can be hindered by the presence of oscillatory phenomena within magnetic wave guides. Returning accurate parameters is crucial to both magnetohydrodynamics studies and solar physics in general. Here, we employ a simulation featuring propagating MHD waves within a flux tube with a known driver and atmospheric parameters. We invert the Stokes profiles for the 6301 $\unicode{0xc5}$ and 6302 $\unicode{0xc5}$ line pair emergent from the simulations using the well-known Stokes Inversions from Response functions (SIR) code to see if the atmospheric parameters can be returned for typical spatial resolutions at ground-based observatories. The inversions return synthetic spectra comparable to the original input spectra, even with asymmetries introduced in the spectra from wave propagation in the atmosphere. The output models from the inversions match closely to the simulations in temperature, line-of-sight magnetic field and line-of-sight velocity within typical formation heights of the inverted lines. Deviations from the simulations are seen away from these height regions. The inversion results are less accurate during passage of the waves within the line formation region. The original wave period could be recovered from the atmosphere output by the inversions, with empirical mode decomposition performing better than the wavelet approach in this task.