For sure, rpm -U does wipe and change information from the .cfg files. I have to hand check them on each upgrade to ensure it’s all right. We have a high number of things “locked down” and it seems like the testing is done with more permissive settings so it’s not seen. Off the top of my head, I know that:
AvailableSessionTypes unix-gnome
Gets wiped with each upgrade and goes back to
AvailableSessionTypes physical-desktop,shadow,unix-xsession-default,unix-gnome,unix-xdm
I also have found the upgrade scripts are adding duplicate entries which are commented out, and the file is getting bigger and bigger.