[2022] Going to settings ingame overriding launcher settings

It is normal that changing the settings in the game overrides a previous setting chosen in the launcher.  

Sorry, I'm a bit lost with your problem now.

You change the game's resolution settings in our launcher, is that right? That writes out to pdx_settings.txt

Then you run the game from the launcher. What happens then? That should copy those new settings to settings.txt  

Antivirus apps can prevent the launcher and game from updating those ..txt files. Which one do you use?

Add CK3.exe to the exceptions list of your antivirus app; ESPECIALLY if you have Windows Defender, add it to the Ransomware "Apps Allowed Through" list.

You should add steam.exe and C:/users//AppData/Local/Programs/Paradox Interactive/launcher-v2.2022.2/paradox launcher.exe to that list.