How to Use an External ST-Link/V2 with the STM32F4 Discovery Board
You'll need to isolate the microcontroller from the st-link portion of the board. To do this just remove the jumpers on the CN3 pins.




Then, to use your external st-link, make the following connections to the microconroller pin headers:


SWDIO -> PA13
SWCLK -> PA14
GND -> GND
VAPP -> 3V/VDD
Do not connect the USB cable


Program it in SW mode.

Not sure why you'd want to do this, unless you wanted to use JTAG to program it instead. If that's the case let me know and I'll update the answer.