Just changing PMODE pins on the FPGA side won't help.
When the FX3 powers up, the PMODE pins needs to be as per the F11 for usb boot. So, you can do it by using hardware pull-ups, or you need to drive the PMODE pins to have the same voltage and logic levels as F11 using FPGA. So, the FPGA can output these lines and drive the voltages on FX3's PMODE pins while the boot.
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