When elf is flashed from Multilink Universal FX debugger, then the bootloader residing in memory area 0x00400000 - 0x0040FFFF is getting erased. How can I partially erase the rest of application with elf file keeping bootloader untouched?
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For instance you may use following option to prevent bootloader are to be touched by programmer:
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Preserve range from 0x00400000 to 0x0040FFFF in your case