Hi,
- empty flash: if your flash programmer allows you to execute scripts before programming, you can write short script which will disable the watchdog. If you can't do that, the only way is to put the SBC chip to debug mode.
- bootloader: there are two options - either disable the watchdog before firmware update or refresh the watchdog periodically. If you use SSD flash drivers, you can use callback function to refresh the watchdog.
Regards,
Lukas