I think I might have solved my problem, but I would like an NXP employee to confirm if truly addresses the problem:
under bd_files/ each .bd file defines what the shadow write application performs which includes setting the flash block configuration in the application images + the flash block configuration provided to the ROM bootloader. In section (0), I make amendments such that the flash block configuration given to the ROM bootloader is the simplified NOR flash configuration, and the flash block configuration given to the images is given the flash configuration block attached earlier, like so:
```
section (0) {
// Configure external memory
load "basic_debug_porta_qspi_nor.bin" > 0x0010C000;
enable @0x9 0x0010C000;
erase 0x08000000..0x08012000; //Erase FLASH
load "flash_config_mx25u6432f.bin" > 0x08000400;
load "gen_sb/image_version.bin" > 0x08000600;
encrypt (0) {
load inputFile > 0x08001000;
}
erase 0x08040000..0x08052000; //Erase FLASH for dual boot image 1
load "flash_config_mx25u6432f.bin" > 0x08040400;
load "gen_sb/image_version.bin" > 0x08040600;
encrypt (0) {
load inputFile > 0x08041000;
}
```
the .sb file seems to be executed appropriately afterwards, and the application seems to function fine. This does mean that I have to call the build_image script in terminal and not through the application, because the application otherwise will change this file.