If you just upgraded from 4.5 to 4.6 it may be that you simply have to reinstall.
I haven't upgraded yet, but I assume this will fix the problem because Xcode is an app and when it installs it removes the old one and replaces it with a new one. The template files are installed directly into the app, and not a shared place external to Xcode (which is why the files get deleted).
Also, I'm not sure about the background updating.