Those are automatically migrated. But if you want to change the old path for your SSL certificates from /home/domain to the new one in /etc/ssl/virtualmin (which is recommended), you can do it after the migration. To do this, go to “System Settings ⇾ Server Templates: Edit Server Template / SSL website for domain” and change the path on the template used by the virtual server. Set “Template for private key path” to a custom path like /etc/ssl/virtualmin/${ID}/ssl.key. Leave “Template for certificate path,” “Template for CA certificate path,” and “Template for combined certificate path” set as “Same directory as key file.”
After making these changes, go to “Manage Virtual Server ⇾ Setup SSL Certificate” and find a button to update the SSL certificates path to match the new path you entered on the template.