Preferential diffusion is very important in simulations of hydrogen flames. Flame stretch and curvature induce strong preferential diffusion effects in laminar premixed hydrogen flames, causing strong local deviations from the unburnt mixture fraction in the reaction zone. In tabulated chemistry methods, this necessitates the use of a partially premixed model even if the inlet mixture is purely premixed. Furthermore, in realistic combustion problems heat losses often play a dominant role. In this paper we derive a preferential diffusion model for constant but non-unity species Lewis numbers using three controlling variables, namely mixture fraction, progress variable and enthalpy. The model has been implemented in the Flamelet Generated Manifold (FGM) approach and validated by comparing with detailed chemistry simulations. As a test case we investigate a 2D laminar premixed hydrogen flame stabilised on an isothermal slit burner. Additionally, the model was compared with the standard treatment of preferential diffusion in FGM to show the increase in accuracy of the new model presented in this paper. The new model shows a significant improvement compared to the previous model, which can be attributed to the inclusion of cross-diffusion. The importance of the additional diffusion terms and its variation in mixture fraction for initially purely premixed hydrogen flames is highlighted.