I haven't had a chance to re-confirm it but I had a feeling your plugin changes:
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteCond %{HTTPS} !=on
RewriteRule ^(.*) https://%{SERVER_NAME}/$1 [R,L]
RewriteRule ^index.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
to
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
everytime it updates. Is that possible or would the reason for that lie somewhere else?
https://wordpress.org/plugins/all-in-one-wp-security-and-firewall/