Changes that you make through the Administrator interface are written to the application_setting table in the application database and take precedence over settings in the XML files. If you want to revert to the values in the XML files, you need to delete the relevant record(s) in the application_setting table.
Note: users can have the last word on preferences settings by making changes through the Preferences dialog box, which they can invoke from the Navigation bar. Thus, the settings that a user specifies in the Preferences dialog box override settings that an administrator has made in the Settings module (which in turn override the defaults specified in settings.xml).
6 IBM Lotus Learning Management System Release 1 Customization Guide