The cost of a hardward failure in high-performance computing systems is usually extremely high because of the system stall where billions of operations can be lost within one second. Thus, implementation of self-restoration mechanisms is one of the most effective approaches to keep system performance on a required level. The project presents a new approach, which allows retaining the performance of the Run-Time Reconfigurable stream processing system on its maximum level. This becomes possible by development of multi-level self-restoration mechanism that consists of: restoration by FPGA-scrubbing, restoration by FPGA-slot replacement and restoration with optimum performance degradation. All above levels of restoration procedure were developed and tested on reconfigurable computing platform based on XILINX Virtex FPGA. Analysis of achieved results of the developed mechanism shows a very fast restoration of functionality and dramatic increase of lifetime of FPGA based computing platforms.