I'd like to add to this, I installed nginx on my Raspberry Pi and was using it on my internal network. I'm not an administrator, just a tinkerer who has no knowledge that the default www share should not be used. Because of this i've lost my index.html that i was using.
I'd assume there are a lot of users like me who are not using nginx in a production environment, and as such i consider this to be a bug. A pretty bad bug that can wipe out someones hard work for absolutely no reason. Why even overwrite the standard index when you upgrade? It seems even more ridiculous than expecting everyone to know not to use the default www.