When a wheel passes over a rail surface irregularity, the resulting vehicle excitations lead to the application of additional system forces to both the track and the vehicle. These forces contribute to an accelerated track geometry deterioration, which in turn results in increased costs. In a recent paper, a clear correlation between the presence of rail irregularities and poor track geometry quality was demonstrated. Rail surface irregularities thereby were quantified by raw data of a chord-based optical measurement system mounted on the regular track recording vehicle in Austria. This paper deals with deconvolution of the recorded data in order to guarantee irregularity quantification without any distortion. Two different deconvolution approaches are developed and validated by additional measurements. Using the deconvoluted data, previously published evaluations were repeated, and the impact of using deconvoluted data instead of chord values was analysed. The correlation between short-wave effects and track geometry quality can not only be confirmed; it is even stronger than predicted by the chord data. The results of the analysis demonstrate that irregularities with amplitudes exceeding 0.08 mm contribute to an accelerated deterioration in track geometry. Amplitudes of a greater severity result in track geometry levels that are up to 120% inferior to the average.