Comment 4 for bug 1436297

A workaround for the missing bookmarks is to is to unlock the nautilus shortcut from the launcher and instead drag across /usr/share/applications/nautilus.desktop and lock that to the launcher (in the files view of that folder three items show as Files, it is the one that is about 600 bytes long that is wanted). Then to fix the duplicate icon problem add to the end of the [Desktop Entry] section of that file the line
StartupWMClass=nautilus