We propose a two-point flux approximation finite-volume scheme for the approximation of two cross-diffusion systems coupled by a free interface to account for vapor deposition. The moving interface is addressed with a cut-cell approach, where the mesh is locally deformed around the interface. The scheme preserves the structure of the continuous system, namely: mass conservation, nonnegativity, volume-filling constraints and decay of the free energy. Numerical results illustrate the properties of the scheme.