Notepad++ Portable 6.5.5 Preferences

How can I keep preferences from being overwritten (presumably by the fact that \PortableApps\Notepad++Portable\App\Notepad++\config.xml is replaced each time the program is launched)? I am not editing the file manually (as this article indicates is fraught with problems).

I also want to save the customisations that I make to the toolbar.