—Flash-based FPGAs are increasingly demanded in safety critical fields, in particular space and avionic ones, due to their non-volatile configuration memory. Although they are almost immune to permanent loss of the configuration data, they are composed of floating gate based switches that can suffer transient effects if hit by high energetic particles with critical consequences on the implemented logic. This paper presents a new way for the analysis of the impact of Single Event Effects in Flash-based FPGAs. We proposed a new methodology to identify the most critical switches inside the configuration logic block and the most redundant and robust configuration selection for each logic function. The experimental results achieved by fault injection demonstrated the feasibility of the proposed method and show that by using the most robust functional mapping it is possible to enhance the reliability of the entire design with respect to a not robust ones.