question about dual-purpose pins used as normal I/O

Thank you for your reply.

I've already hard-wired the nCONFIG, CONF_DONE pins to control other components as the output pins, and the nSTATUS pin as GPIO connecting with another MCU. They are already used as the user I/O on the PCB so I think that option may conflict with the hardware.

However, I've made an experiment that I jumped wire the nCONFIG, CONF_DONE to 3.3v through 10k resistor, then the FPGA can run successfully after reboot. I think these two pins should better be left alone and pull-up for the next version.