The homepage loads, but every post and page says "Not Found". Your content is still there. The server has stopped passing pretty links to WordPress.
# BEGIN WordPress and ends # END WordPress. If the file is missing or empty, the permalink save will recreate it when the folder is writable.AllowOverride All for the site folder and mod_rewrite switched on (sudo a2enmod rewrite, then restart Apache).try_files $uri $uri/ /index.php?$args; inside location /.?p=123 links, the rewrite rules are the only problem.If none of that brings the pages back, send me the address and I will check which links fail and why.
Want the rest of your site checked after it is back? Run a free 40-point check at tinkeraudit.com.