Abstract In this work, we propose a new method to fill the gap within an incomplete turbulent and incompressible data field in such a way to satisfy the topological and intensity changes of the fluid flow after a non-parameterized geometrical variation in the fluid domain. This work extends the one that has been published as a conference proceeding to the 2018 AIAA Scitech Forum and Exposition (Akkari et al. in Geometrical reduced order modeling (ROM) by proper orthogonal decomposition (POD) for the incompressible navier stokes equations. In: 2018 AIAA Aerospace Sciences Meeting, AIAA SciTech Forum, (AIAA 2018-1827), 2018). A single baseline large eddy simulation (LES) is assumed to be performed prior geometrical variations. The proposed method is an enhancement of the Gappy-POD method proposed by Everson and Sirovich in 1995, in the case where the given set of empirical eigenfunctions is not sufficient and is not interpolant for the recovering of the modal coefficients for each Gappy snapshot by a least squares procedure. This happens when the available data cannot be written as an interpolation of the baseline POD modes. This is typically the case when we introduce non-parameterized geometrical modifications in the fluid domain. Here, after the baseline simulation, additional solutions of the incompressible Navier–Stokes equations are solely performed over a restricted fluid domain, that contains the geometrical modifications. These local LESs that we will call hybrid simulations are performed by using the immersed boundary technique, which uses of a fluid boundary condition and the baseline velocity field. Then, we propose to update the POD modes using a local modification of the baseline POD modes in the restricted fluid domain. Furthermore, we will propose a physical correction of the latter enhanced Gappy-POD modal coefficients thanks to a Galerkin projection of the Navier–Stokes equations upon the new modes of the available data. This enhancement procedure on the global velocity reconstruction by the physical constraint was tested on a 3D semi-industrial test case of a typical aeronautical injection system and, a 2D laminar and unsteady incompressible test case. The speed-up relative to this new technique is equal to 100, which allows us to perform an exploration of two new designs of the aeronautical injection system.