I've been having an intermittent issue with odd code being written to the .htaccess file which breaks the site - either incomplete code, 100's of lines of extraneous code, or total removal of the WP code. This comes with no warning, but does seem to be linked to times when we have a sudden increase in lockouts.
Please, please, please can you review this issue, as it's a serious issue and I have found others who are experiencing the same problem and need it to be reviewed.
I've posted details in the forum here: http://wordpress.org/support/topic/rewrite-to-htaccess-file-shut-down-site but have had no feedback or support for it. I would post it in a Bug report section if I could find one - but I can't, so have to post here. I shall redirect people from my full post to here, so they can find a solution too...