Apache2 is deleting .htaccess & after causing to Internal Server Error

Question

I have a problem. I've installed apache2 on debian 6, configured MaraDNS and add SSL, but I have got a problem. Apache2 is deleting .htaccess file. When I upload .htaccess to server via FTP and refresh there isn't .htaccess file. Next, when I want to change Permalinks from %postname% to p=$id I get Internal Server Error and this error shows all the time(trying restart apache2 doesn't work).

error.log shows

[Thu Jul 04 02:58:10 2013] [alert] [client 188.95.29.167] /var/www/.htaccess: Expected </link> but saw </head>
[Thu Jul 04 02:58:10 2013] [alert] [client 188.95.29.167] /var/www/.htaccess: Expected </link> but saw </head>, referer: https://domain.me/wp-admin/post.php?post=1&action=edit

Edit - I deleted .htaccess file(one contains some HTML code - something must overwrite it). But now all tables in mysql is deleted

Answer 1

Your .htacces is not gone, just hidden (*nix hides files by prepending them with a dot). Set your FTP client to show hidden files and you'll find it.

Also, your .htaccess file is invalid, hance the error and log lines.