When yum installs a newer RPM it will do one of three things about the .conf file (if any).
1) if the .conf file doesn't have any changes, it'll leave it alone.
2) if the .conf file has a required change, and the updated program won't run without the change, then the old .conf file will be saved as ~.rpmold and the new file installed as the .conf file.
3) if the .conf file has a non-required change (but the change may add functionality), then the new .conf file will be saved as ~.rpmnew and the old .conf file will be left alone.
So your job is to make sure any new lines adding functionality are installed in the .conf file, if you want the functionality.
And if the old file is saved as ~.rpmold and the new file is installed as .conf your job is to make sure any custom lines installed by you or by DA in the old .conf file are moved to the new file.
Jeff