In this paper we propose an automated design flow for the implementation of autonomous fault-tolerant systems on SRAM-based FPGA platforms, able to cope with the occurrence of both transient and permanent faults. The goal of the proposed methodology is to increase the system's lifetime, by designing it able to detect and mitigate the effects of soft errors, as well as of permanent, non-recoverable ones, by exploiting dynamic reconfiguration. The application of the hardening design flow to a real case study is reported, to validate the methodology