I have a problem when using JLinkExe + JLinkRTTClient. My operating system is Ubuntu 18.04, and I compile the project using cmake and gcc (using great helper scripts from nRF5-cmake-scripts).
Recently I have updated to SDK v. 17, I do not know if that is related, and also I have updated Nordic Command Line Tools from version 10.6.0 to the latest 10.12.1.
The problem now is that if I launch the JLinkExe and JLinkRTTClient with nRF52840 chip connected via SWD, I can correctly see the initial output of my application in JLinkRTTClient, and I can check that it send it again by hardware resetting it.
The problem is that after I re-flash using nrfjprog the chip (either application only, or application + softdevice + bootloader), the JLinkRTTClient stops showing any output. To restore correct operation, I either have to re-launch JLinkExe + JLinkRTTClient, or type "connect" command in JLinkExe so that it reconnects again - after that I see the output in JLinkRTTClient again.
What can be the cause of the problem?
In the attachments below are my configuration files (app_config.h and sdk_config.h).

