I understand you used our HTTPS configuration tool to generate the certificates, right? Why don't you run it again to generate a new certificate with the new domains?
Regarding the changes in the configuration, the httpd-vhosts.conf file is not included by default in the Apache's configuration file. Once you edit the file and ensure the certificates are properly generated and configured, you need to include that file in the Apache's bitnami-apps-vhosts.conf file
We will update our documentation to include that information