I'm running version 3.3 of Better WP Security. This morning, Better WP Security updated the .htaccess file (in order to ban an IP address). After the update the .htaccess contained only the section for Better WP Security and the rest of the .htaccess file content was removed. Since the WordPress rewrite rules were removed nobody was able to access the articles (clicking on the links for the articles gave a 404 error). I restored an older version of the .htaccess file in order to fix the problem. I then unchecked the box so that Better WP Security will not update the WordPress core files.