the rules are defined in the webassist/security_assist/helpergroupsrulesphp.php file.
Dreamweaver expects to find this file at the root of your dreamweaver site.
since you have changed the root, it is no longer in the correct place. move that file to the new DW Site root.
for the WebAssist menu:
Delete the Dreamweaver Cache file from the users configuration folder:
If that does not de the trick, then uninstall Security assist and reinstall it, it will not effect the rules.