Your host has changed something in the site config files and created this problem. If your links are correct in your html I doubt there is anything you can do.
You might be able solve the problem by making them absolute if they are now relative.
relative link = ./filename.html or filename.html or directory/filename.html
absolute link = sitename.com/filename.html or
www.sitename.com/filename.html
Making them absolute places an additinal burden on the server but will solve some problems. It is usually a necessity when dealing with sub-domains.