Commercial off-the-shelf (COTS) reconfigurable devices have been recognized as one of the most suitable processing devices to be applied in satellites, since they can satisfy and combine their most important requirements, namely processing performance, reconfigurability and low cost. However, COTS reconfigurable devices, in particular Static-RAM Field Programmable Gate Arrays (FPGAS), can be affected by cosmic radiation, compromising the overall satellite reliability. Scrubbing has been proposed as a mechanism to repair faults in configuration memory. However, the current scrubbing mechanisms are predominantly static and unable to adapt to run-time variations in applications. In this paper, a dynamically adaptive scrubbing mechanism is proposed. Through a window-based scrubbing scheduling, this mechanism adapts the scrubbing process to the reconfigurations and modifications on the FPGA user-design at runtime. Conducted simulation experiments show the feasibility and the efficiency of the proposed solution in terms of system reliability and memory overhead.