Since I cannot raise a Intel support request for fpga's without a Premium Support account I thought I'd try 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.