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I'm using external watchdog timer in my board to reset the MK64 in case no strobe is passed to it (I know there's also internal watchdog in the MK64). What I don't understand is what should happen while burning the internal flash of the MK64. Since no strobe will pass to the watchdog timer, the watchdog will reset the board all the time (in loop).

Any idea how to avoid such scenario?

(I've placed pull up resistor on the PB_RST (pushbutton reset pin) but that will not help in case of burning the flash).

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use a jumper between the external watchdog timer to MK64 reset pin, place the jumper on normal use and remove when flashing the device,

If you are using USB to flash the device add a circuit to sense the USB +ve supply to disable the external watchdog timer output

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