@datakick Late answer
Its very common when you have many domains on your mailserver that you create one cert for all the domains by making lets encrypt create the same cert for multiple domains. its nothing that compromize security but when you get 20-30 domains on the email server it a pain in the but to keep track of all the different serts if you create them one by one.
The problem here seems not to be the same. The php mailer works without a problem sendig out mails to customers, but the mail alerts, which I assume also use Php Mailer does not. So hardly the cert cant be the problem
I will test the code change