The application will not run during update. The bootloader is standalone. Device will always start the bootloader first and if it receives command to start updating it will stay in bootloader, otherwise it will run application. If i write application's vectors in boot sector, and than swap them, bootloader will not run after reset. My plan was to have application's vectors at 0x2000+vector address, and then in bootloader area, when interrupt is called just jump to address in application vector table at 0x2000+.
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