This paper presents the design of a reconfigurable avionics system based on modern Static Random Access Memory (SRAM)-based Field Programmable Gate Array (FPGA) to be used in future generations of nano satellites. A major concern in satellite systems and especially nano satellites is to build robust systems with low-power consumption profiles. The system is designed to be flexible by providing the capability of reconfiguring itself based on its orbital position. As Single Event Upsets (SEU) do not have the same severity and intensity in all orbital locations, having the maximum at the South Atlantic Anomaly (SAA) and the polar cusps, the system does not have to be fully protected all the time in its orbit. An acceptable level of protection against high-energy cosmic rays and charged particles roaming in space is provided within the majority of the orbit through software fault tolerance. Check pointing and roll back, besides control flow assertions, is used for that level of protection. In the minority part of the orbit where severe SEUs are expected to exist, a reconfiguration for the system FPGA is initiated where the processor systems are triplicated and protection through Triple Modular Redundancy (TMR) with feedback is provided. This technique of reconfiguring the system as per the level of the threat expected from SEU-induced faults helps in reducing the average dynamic power consumption of the system to one-third of its maximum. This technique can be viewed as a smart protection through system reconfiguration. The system is built on the commercial version of the (XC5VLX50) Xilinx Virtex5 FPGA on bulk silicon with 324 IO. Simulations of orbit SEU rates were carried out using the SPENVIS web-based software package.