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We describe In-Place Reconfiguration (IPR) for LUT-based FPGAs, an algorithm that maximizes identical configuration bits for complementary inputs of a LUT thereby reducing the propagation of faults seen at a pair of complementary inputs. Based on IPR, we develop a fault-tolerant logic resynthesis algorithm which decreases the circuit fault rate while preserving functionality and topology of the LUT-based logic network. Since the topology is preserved, the resynthesis algorithm can be applied post-layout and without changes in physical design. Compared to the state-of-the-art academic technology mapper Berkeley ABC, IPR reduces the relative fault rate by 48% and increases MTTF by 1.94Ã with the same area and performance, and IPR combined with a previous fault-tolerant logic resynthesis algorithm (ROSE) reduces the relative fault rate by 49% and increases MTTF by 2.40Ã with 19% less area but same performance. The above improvement assumes a stochastic single fault and more improvement is expected for multi-fault models.