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I am assuming you have already done the necessary modification required in 43xxx_Wi-Fi/WICED/platform/MCU/BCM4390x/peripherals/spi_flash directory. If you have done that, you can look into the waf.sflash_write app and the .tcl script. A good point of debugging the issue will be enabling #define DEBUG_PRINT macro which should give you some idea about the responses.
Thank you for your comments.