There is no fixed pin mappings for Flags to GPIO pin. You can choose to map a Flag to any of the available GPIO pins in GPIF II Designer tool. However some GPIO pins are reserved and cannot be used as flags. For eg: GPIO 17 is fixed for GPIF Interface CLK, GPIO 0-15 for 16 bit data bus and so on.
Refer Application Note AN65974 http://www.cypress.com/?rID=51581 which explains how to configure flags in FX3.
Small correction: Its GPIO 16 for GPIF clock interface clock and not GPIO 17.