When you add a domain to the MyVestaCP control panel, you select a Proxy Template for the domain. By default, the Proxy Template is 'hosting'. If you want to permanently keep your changes in the NGINX configuration file for a domain, you need to modify the template files for your selected Proxy Template. Those template files can be found inside the folder:
/usr/local/vesta/data/templates/web/nginx
Suppose you want to add IPv6 to the NGINX configuration files; you will have to modify two template files: hosting.stpl (for *.nginx.ssl.conf) and hosting.tpl (for *.nginx.conf).
Open hosting.tpl in an editor and make the following change for IPv6.
listen [your_ipv6]:%proxy_port%;
Open hosting.stpl in an editor and make the following change for IPv6.
listen [your_ipv6]:%proxy_ssl_port% ssl;
After these changes in the template files, your configuration will always have an entry for IPv6. So, whenever the NGINX server is updated, you do not have to manually update domain-specific configuration files.