.htaccess file changes disappear

I was having a similar problem recently. It turned out it was due to a code injection in the /wp-includes/nav-menus.php file. There was a Base64 malware code injected that was causing my .htacess file to chmod itself to 444. Something called some kind of darkleech malware. See this link for more, maybe it’s what’s happening in your case as well: https://blog.sucuri.net/2015/03/pseudo-darkleech-server-root-infection.html

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