Once I program the SBC(to normal mode) it seems that the watchdog turns off the microcontroller power supply, and this causes that I can't flash my microcontroller anymore, I don't know if there is a way to avoid this and keep flashing the micro normally
You can pullup RESET line while programming/debugging either on board or on debugger.
By doing this, You are good to go for flashing/debugging and when you would like to check full functionality, You can remove pullup and SBC will take control over it.