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fromelf.exe generate two bin file

When i produced two bin(one and second) file with mdk tools fromelf.exe,the difference of the two bin files is the second bin file only more than a single one code in source project. so when i compare the two bin files in hexeditor,the two file has many differences. I want to find the difference between the two files,and update the difference into stmf10x flash,but the two bin file has many difference,is this way whether could solve the problem,please help me. thanks