I just had this happen for the second time. My .htaccess was truncated in the middle of the last Rewrite Rule, and the error logs were giving a repeated error "Invalid command 'Rew', perhaps misspelled or defined by a module not included in the server configuration". I concluded that it must be Wordfence as I haven't seen any other plugin writing to .htaccess.
It happened 2 or 3 weeks ago as well, to a different site. I keep my plugins up to date.