Toni,
I fear I do not understand. If you run the full installer in maintenance mode (without an uninstall) then it does not touch your configuration at all. It just brings your installed version to the latest build. And a "web update" never touches your configuration settings.
Only if you uninstall first and you answer the question "Delete all files and folders that are under %APPDATA%\Lindersoft\SetupBuilder 7?" with YES then it will remove your config file.
Friedrich