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The locations of the different datasets in the external flash is specified in the apps lookup table (wiced-sdk/WCIED/platform/MCU/wcied_app_lut.c) which is always placed at offset zero in the external flash. I suspect the reason why your prototype board isn't working is because you're probably not flashing the APPS.bin file to the first sector of the external flash. The APPS.bin file is located in wiced-sdk/build/(project-name)/APPS.bin and is generated when you build your project.
It would be nice if the build scripts created a text file with the addresses of the objects in the flash. I do what you're doing though... I just note what the address is when I run download_apps and include those values in by production build script... I suspect it wouldn't take much to modify the build script (wiced-sdk/tools/makesilfes/wiced_apps.mk) to spit out that file...