Shape optimization with respect to the suppression or enhancement of dynamical flow structures is an important topic in combustion research and beyond. In this paper, we investigate the flow in an industrial fuel injection system by experimental means, as well as large eddy simulation (LES) and linear stability analysis (LSA) for two configurations of the swirler. In the first configuration, the reference geometry, a precessing vortex core (PVC) occurs. In the second configuration, a center body is mounted in the interior of the injector. It is shown by both experiments and LES that the PVC is suppressed by the presence of the center body, while the mean flow remains nearly unaffected. The method of LSA is applied in order to explain the effect of the geometry change. The work shows that LSA is capable of explaining the occurrence or disappearance of coherent structures evolving on the turbulent flows if the geometry is changed. This is an important step in using LSA in the context of shape optimization of industrial fuel injectors.