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Unable to use Debug out on nRF 52840 dev kit to program nrF 52840 usb dongle

Hi,

I am trying to debug firmware on the nRF PCA10059 usb dongle board, through a nRF10056 dev kit by attaching a standard 10 pin header on the usb dongle at P1 & connecting it to the Debug out 10 pin header on the dev kit through a 10 pin ribbon cable.
SB47 on the dev kit board is shorted so as to only debug the usb dongle & not the nRF chip on the dev kit, if using the Debug out from the dev kit (using Segger Embedded Studio).

I am doing the following steps & observing the following behaviour:

Compile a firmware for PCA10059.
Program usb dongle by connecting it to PC with USB & programming with nRF connect software.
Works.

Disconnect PCA10059 dongle from PC usb & connect to dev kit Debug Out through 10pin cable & power up the dev kit.
Try debugging same firmware on PCA10059 through Segger Embedded Studio using dev kit Jlink through debug out.
Works.

Change a print statement in the code.
Try loading & debugging same firmware through Segger Embedded Studio using dev kit Jlink through debug out.
Does NOT Work. Red LED on usb dongle flashing.

Connect PCA10059 back to PC using usb.
Program new firmware to usb dongle with change in print through nRF connect software through usb.
Works again.

Disconnect PCA10059 dongle from PC usb & connect to dev kit Debug Out through 10pin cable & power up the dev kit.
Try debugging same firmware through dev kit Jlink through debug out.
Works again.

What am I missing to do, while using the Jlink on the dev kit, that the nRFConnect software is doing while programming the dongle? I am unable to make changes in firmware & directly reload code on the dongle & have it work. I have to program it first through the nRF connect using usb, to be able to connect & use the Jlink later.

Regards.

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