We propose a workflow for updating 3D geological meshed models to test different layering scenarios and to assess their impact on the simulation of injection. This workflow operates on a tetrahedral mesh that encodes rock unit information as well as rock physical properties. The alternative layering meshes are built by modifying the input mesh and inserting a new horizon defined by a scalar field. Modifying consistently a 3D meshed model while keeping its quality is a challenge that we tackle using the advanced capabilities of MMG, an open source remeshing library. injection is then simulated with GEOSX, an open-source, multiphysics, and multilevel simulation solver. We demonstrate this workflow for stratigraphic layering uncertainty assessment on a simple synthetic layered reservoir on the flank of a salt diapir. Comparison of simulation results is eased since modifications of the mesh are localized to the area around the inserted horizon. The consistent results highlight the role of stratigraphic unconformities for trap integrity. This work opens a promising path for developing numerical simulation of injection on unstructured meshes by combining advanced coupled flow-geomechanical models in geological domains affected by structural uncertainties.