The configuration-xml that one receives via backup in WebUI can be reduced to a few settings-sections that are useful for your use-case. When you provision this reduced set, only the settings-sections listed will be affected.

  <configuration>
    <identities>..</identities>
    <keys>..</keys>
    <!--telephony, contacts and all the other sections are not part of this settings-patch-file and thus will not be affected-->
  </configuration>

When you only need to make changes in a single settings-section you may drop the configuration-tag:

  <!--<configuration> not needed when only a single settings-section is provisioned-->
  <keys><!--only make changes to the keys-section--></keys>