I actually put forward something similar but instead of writing the Flash it bites it directly to another FPGA with a wide parallel bus slave SelectMAP. Another option is to change the binary file to install WBSTAR and turn on reset using IPROG to release the load of the golden setting and immediately try to load the main setting. I think you might need to set it up so that FPGA always supports golden settings then golden settings try to reset FPGA and download the other to write ICAP primitive.In this case you do not have to do anything special Once you have finished create a bit file just create it as you would if you were using FPGA directly through JTAG. I can write SPI flash through an Ethernet interface so I think it could write bitstream to blink over Ethernet so I could program FPGA over the network without using a JTAG cable.
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