Hello,
I just wanted to let you know that just a few minutes ago the same happened to me. The site produced a 500 script error and was not available untill I changed the .htaccess file. I am using WP Super Cache at the same time, but Better WP Security deleted all permalink rewrite rules from WordPress and all entries from the cache plugin.
I have currently disabled this plugin. Any suggestions? I still would like to use it, but I also don′t want ro risk to break the site again.