It reprograms the Xilinx logic chip, which handles the clocks, s/pdif, and DAC interface. If you remember older computer used to have dozens of 14-pin or 16-pin chips with 74xxxx part numbers. Modern systems use programmable chips (CPLDs or FPGAs) in place of these. They are smaller, less expensive, quicker to design, and allow the circuit to be reconfigured in software. Kind of like having a custom chip that you can change whenever you want.
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