I checked your shared chat log and found following entries related to issue.
If any update will overwrite the .htaccess file in the sites, this will happen
Theme and plugins don’t update this file and only WordPress update may overwrite it but most of the time it is preserved by WordPress.
If the theme or plugins updates not compatible with php shown in .htaccess that will show 500 error
I have installed the php 5.6 now.
Before making any update you should confirm if that update compatible with php 5.6
The WordPress itself need PHP version 7.2 or greater as described in this page https://wordpress.org/about/requirements/ and also the PHP version 5.6 that you are using is not supported anymore as described here http://php.net/supported-versions.php so please update PHP version on your server to avoid this issue.