In this work variations of the carrier lifetime in a GaInAsP/InP quantum well in two-dimensional PhC structures etched by Ar/Cl-2 chemically assisted ion beam etching as a function of the processing parameters is investigated. It is shown that the deposition conditions of the SiO2 mask material and its coverage as well as other process steps such as annealing affect the carrier lifetimes. However the impact of patterning the semiconductor on the carrier lifetime is dominant, showing over an order of magnitude reduction. For given PhC lattice parameters, the sidewall damage is shown to be directly related to the measured carrier lifetimes. A simple qualitative model based on sputtering theory and assuming a conical hole-shape development during etching is used to explain the experimental results.