Do you have a list of the settings you are trying to write and in which files/sections exactly?
Normally the launcher ignores (and leaves there) any setting it does not know about, but obviously it could be buggy
That being said, the game server itself is known to rewrite the ini files and remove what it does not like, so one thing you could try (just to make sure) is to launch the server with the launcher, just to make sure it’s fully updated, etc… then shutdown the server, quit the server launcher, modify the ini files, and then manually (without the launcher) start the game server again, and when the server is running, check if your changes are still in the ini file, then cleanly quit the server, and check again.