Hi @Ade,
Once you modify a template, you must rebuild the web domain to apply the changes.
From GUI:
From command line:
v-rebuild-web-domain USER DOMAIN [RESTART]
Example using test as user, example.net as domain and yes to restart the web services.
v-rebuild-web-domain test example.net yes
Also, keep in mind that /usr/local/hestia/data/templates/web/nginx/php-fpm/ templates are for Nginx standalone, if you are using Nginx+Apache, the proxy templates are her /usr/local/hestia/data/templates/web/nginx/ and apache templates here /usr/local/hestia/data/templates/web/apache2/php-fpm/