Wrong flash connections

Pin C1 is dedicated to ASDO signal which must be wired to EPCS ASDI pin in AS configuration mode. Since this is a FPGA fixed function active before user configuration, you can't swap it to another pin. I'm afraid you probably need to change the pcb or find a way to connect the signal to the right place.

Please note that if you only needed to program the flash (and not to configure from it), you could have done it, since AFTER configuration you can route the proper signals to gpio pins. But in this case you should have used a custom jtag flash programmer, since the standard one assumes epcs is connected to C1.