Do you have a backup of the site that you can revert to? Does the site that is live now have the problems in it? If so did you completely overwrite the good version with the newer corrupted one?
One thing that you could try it to define a new Dreamweaver site and copy into it your Template folder from your existing site. Make sure that you do not have any check in or check out functionality enabled for the site. You should be able to go to Site > Modify SiteAssist Site. This should allow you to create a new site based on the settings that you have for the site. Give this a try to see if you can get all of the pages generated correctly this way. If so you should be able to import a copy of your site into this new DW site and update it there.