Adding or removing domain names from a certificate causes them to be treated separately when it comes to expiration notices. See the documentation for details, specifically:
If your certificate is already renewed, we won’t send an expiry notice. 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.