If your gamelist.xml is being over written you can check to see if you have "save meta data on exit" enabled (press your start button and go to 'settings' If I recall coreectly). If you do not disable it, emulationstation will overwrite your manual XML entries. Turn it off before you jump to prompt or ssh in to edit your game list.xml. You will also need to restart in order for your manual entriesnto appear as well.
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