As you have noted the editing of a Site Sculptor site with CSS Menu Writer will cause the menu files to be overwritten. This is one reason we do not suggest using menu writer to update the menu on the completed site. Rather than update the existing menu you should be generating a new Site Design for Site Sculptor based on the menu you would like to include.
You can then quickly and easily create a new site based on the new design. What Site Sculptor generates should be a site with the pages, templates, and menus existing for you. You can then customize the site or update the contents via the content management.