Yes, this shoud work. You have to reconfigure the GPIF Matrix. This is descriped in some other postings here in the forum.
I do this another way: Sinse there is a FPGA in the system, I connected the SPI Flash pins to the FPGA also and so I´m able to reprogram the flash via the FPGA without changing the FX3 config.
If you are looking for the piece of code that does the re-configuration of GPIF II then please refer to the following application note: