SiteScope stores master.config information not just in master.config text file but also within __masterConfig persistency object.
When some changes are not reflected automatically, one may need edit both places to make them consistent when the service is stopped.
a. Edit <SiteScope installation>\groups\master.config using any text editor.
b. Edit persistency using <SiteScope installation>\bin\PersistencyViewer.bat
Filter by Type: com.mercury.sitescope.platform.configmanager.MasterConfig