Question: My WordPress.com site’s menu links are still connected to the live site after download. Why?
Answer: If yourdomain.com is hosted on wordpress.com, then their system is using also using yourdomain.files.wordpress.com as an Additional Root URL.
In Web2Disk 4, add http://yourdomain.files.wordpress.com (replacing “yourdomain” with your website’s domain name) in Advanced Project Settings > Root URLS > Additional Root URLs.