Bitnami AWS LAMP stack Bncert tool using new certificate for all domains

I am using the AWS Bitnami LAMP AMI on AWS to host multiple WordPress and PHP sites. I am having an issue when I generate a new SSL certificate for a domain using the BNCert tool it’s updating all the vhost apache configuration files for all the other domains to use this certificate which invalidates it on those websites, the server has one IP address and I am using vhost files to configure all the domains.

This is how I am configuring the vhosts in apache:

<VirtualHost *:80>
ServerName example.com
ServerAlias www.example.com
DocumentRoot /opt/bitnami/apache2/htdocs/example.com
<Directory “/opt/bitnami/apache2/htdocs/example.com”>
Options -Indexes +FollowSymLinks -MultiViews
AllowOverride All
Require all granted
</Directory>
</VirtualHost>