This is the reason that you received a certificate expiration email and it's a very common source of confusion The "update" created a new, separate certificate. It isn't a renewal of the previous one because the set of names differ.
We consider a certificate to be renewed if there is a newer certificate with the exact same set of names, regardless of which account created it. If you’ve issued a new certificate that adds or removes a name relative to your old certificate, you will get expiration email about your old certificate. If you check the certificate currently running on your website, and it shows the correct date, no further action is needed.
Just a small misunderstanding If the certificate being served by your webserver has the correct names/validity period you can safely ignore the expiration warning you received.