ATLAS is a global Chemical Transport Model (CTM) with stratospheric chemistry and Lagrangian transport and mixing. ATLAS features a stratospheric chemistry module including 170 reactions, 46 species, a detailed treatment of heterogeneous chemistry and Lagrangian denitrification. Uncertainties in theory and observations of polar ozone depletion and limitations in the implementation of Chemistry and Transport Models (CTMs) are an issue that is often neglected. Here, stratospheric chemistry and denitrification are simulated for the Arctic winter 2009/2010. Several sensitivity runs are used to explore the impact of uncertainties in chlorine activation and denitrification on the model results. In particular, the efficiency of chlorine activation on liquid aerosol versus activation on nitric acid trihydrate clouds is examined. Additionally, the impact of changes in reaction rate coefficients, in the particle number density of Polar Stratospheric Clouds, in supersaturation or the extent of denitrification are investigated. Results are compared to satellite measurements of MLS and ACE-FTS and to in-situ measurements onboard the Geophysica airplane during the RECONCILE measurement campaign. It is shown that even large changes in the underlying assumptions have only a relatively small impact on the modeled ozone loss, even though they can cause considerable differences in chemical evolution and denitrification. Additionally, we show first results from the winter 2010/2011, an exceptionally cold winter, which showed unprecendented ozone loss for the Arctic.