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I can only guess something is stopping CK3.exe from writing out to the Documents/Paradox Interactive/Crusader Kings III/ folder. Make sure it is in all the exceptions lists of your antivirus app.
 
Make a new Windows user profile on this PC and try the launcher/game under that. Any better?
 
Also its doing the same stuff if i try to launch the game over NVIDIA App with changed settings there
Well yes, GeForce Experience and the Nvidia app can overrule the game's own settings, best to not be running them while we work on this.
 
I have no idea what is causing this to you. What if you manually edit those files, do they stay edited?
 
The only graphics setting that resets for me is Refresh Rate, but that's been an identified issue before PDX haven't fixed for half a year when I finally noticed. Not sure about the rest.