I am using a Cyclone V GX part in AS configuration mode using a EPCS128 prom. I cannot program the prom with the generated .jic file. I know the jtag interface is good as configuring the fpga with the .sof file works. I have discovered on my board the CS pin from the EPCS connects to the AS_DATA2 pin AA5 on the Cyclone V and the nCSO pin R4 is not connected. Unfortunately there is no via to pin R4 to connect a flywire. Is there anyway to reprogram/ re-configure pin AA5 (AS_DATA2) on the cyclone to behave as nCSO? Or do I have a complete show-stopper here?
I don't think so. The config pins are dedicated during power on configuration (hardwired in the FPGA) and the only control you have is through MSEL pins.
If you could get to the config pins on the FPGA, you could remove the EPCS chip from the board and "daddy long legs" jumper it for now. But it sounds like you can't get to them.
We spent alot of time looking at config issues since we wanted to change from physically huge and expensive Altera parts to a Winbond chip (sounds like 18.1 supports other options). Everything has to be correct. For example, make sure your power rails follow the recommendations etc.