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What is needed in NCS/Zephyr to make nRF52840 module (Fanstel BC840) to use RC instead of external crystal?

Hi,

We've been developing our prototype with nRF52840DK. Our Zephyr RTOS based code is working fine there with BLE connections and sensors. 
Lately we've been testing our code on our own PCB designs and running into problems with software booting and freezing or BLE connections and advertisement packets dropping.
In particular, the BLE connection drops immediately after hitting connect on the nRF Connect mobile app.

After searching, I found discussions here on devzone like this that hinted at the lack of external crystal is the problem.
I have tested a barebones nRF beacon example from nRF5SDK 17.0.2 by adjusting the LFCLK source to internal RC. The advertisements now come in regularly. I have yet to test the connections there.

My question is: Is there a possibility to change the clock source to RC in Zephyr and how? Are there any other things to consider in Zephyr-based development when moving to the target module?

For context, I have been flashing the firmware to our modules with nrfjprog by using --eraseall followed by s140 and app.
As I understand zephyr.hex contains all that is needed to boot and run the app so is that all I need to flash?

Setup:
Linux
NCS 1.4
Zephyr 2.4
Fanstel BC840-V1 nRF52840 module

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