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If the binary was correctly generated, you should be able to use samba to write the whole file to flash 0. Flash0 and flash1 is contiguous. It is possible with SAMBA to write a file larger than 128k to flash0. The section larger than 128k will then be put in flash 1.
If you really want to hard seperate the binaries, it is also possible to compile 2 projects, with the output elf of the first project as an input to the second compilation so that the second binary/program can make use of the first ones functions. The first binary/program will unfortunately then not have access to the functions of the second binary.
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