When you want to edit configuration settings for My webMethods Server, you download the appropriate configuration file from the MywebMethodsServer database component to the My webMethods Server installation and make the changes in that file. You can then either upload the file to the database component and delete it from the file system, or keep it in the file system so its settings will be used in preference to the equivalent settings in the database.

Go to the old_Software AG_directory\MWS\server\instance_name\config directory and check for any such files. If you do not want such files to be migrated to the new installation, delete them from the old installation.