Hello. Can you please explain one more time, since I am super confused.
Let’s encrypt added mysite . com and www . mysite . com to the whitelist.
I created two certificates for both mysite . com and www . mysite . com.
I created two Virtual hosts for both mysite . com and www . mysite . com with different SSLCertificateFile, SSLCertificateKeyFile, SSLCertificateChainFile, and ServerName.
I use it for Drupal web site with .htaccess settings:
If I check it (non www url) through ssllabs it says : Prefix handling - Not valid for “mysite” - CONFUSING
OR it is better/easy to have one Virtual host and add ServerAliaswww . mysitec . com. In this case I should use certificate for www or non-www version?
You can use multiple domains in one cert by making use of multiple 'Subject Alternative Names' in the X509v3 certificate.
As an example you could request one single certificate that is valid for multiple domains.