It has been quite a while since i updated my Kobo Nia, and with my brain disengaged (enjoying some music obviously), I was using NiLuJe's one-click installer and stupidly replaced the .kobo folder

(i.e. all contents of .kobo replaced by the one-click installer KoboRoot.tgz). NiJuLe's instructions are clear and I should have used the install script but forgot, was distracted etc. This is 100% operator error and I very much appreciate all the tools and the hard work that is obviously placed in them.
What can I do to get back to a working system? I haven't ejected my Nia yet, but I think the .kobo folder is critical for the system and don't really know what I can do other than bang my head on my desk shouting idiot...