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This paper presents an enhanced design flow for the implementation of hardened systems on SRAM-based FPGAs, able to cope with the occurrence of Single Event Upsets (SEUs). The framework integrates three strategies independently designed to tackle the problem of SEUs; first a systematic methodology is used to harden the circuit exploiting an enhanced TMRbased technique, coupled with partial dynamic reconfiguration. Then, a robustness analysis is performed to identify possible TMR failures, eventually solved by a specific local re-design of the critical portions of the implementation. We present the overall flow and the benefits of the solution, experimentally evaluated on a realistic circuit.