Reassuring fault tolerance in computing systems that contain FPGA devices is the most important problem for mission critical space components. With the rise in interest of commercial SRAM-based FPGAs, it is crucial to provide runtime reconfigurable recovery from a failure. In this paper, we propose a superimposed virtual coarse-grained reconfigurable architecture, embedded with on-demand three level fault-mitigation technique. The proposed method performs run-time recovery via discrete microscrubbing. This approach can provide up to 3 faster runtime recovery with 10.2 less resources in FPGA devices, by providing integrated layers of fault mitigation.