If your nginx hosted homepage somehow reverted back to the default, your package manager is putting the original index.html back in there after you update. Your nginx.conf file probably still has this line in it:

root   /usr/share/nginx/html;

Just put your website somewhere that isn't html/ and point the root at that instead. Somehow I didn't notice this because I would update and reboot right before putting up new blog posts, which would then overwrite the packaged index.html with my own.