Programming External Board using NRF52840-DK

I am using the NRF52840-DK REV2 to program my custom board. I am using the debug out port and connecting it to my custom board, I tried both powering the custom board through the DK or externally, I even shorted the SB47 and still having the same issue. I can't get any debug messages on my terminal after "Starting target CPU". I'm using the NRF connect sdk v2.0.0.

Here is what the issue is

When I flash the software (Just a simple blinky) I get no results, the terminal says flash successful. but the LED doesn't blink.

When I use debug mode, the LED blinks correctly. I can disconnect the custom board from the DK and the led still blinking, I can reset the board and the LED still blinking, I cannot disconnect the board and reconnect it, if I do that it no longer blinks. Can someone explain what is this?

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