I receive some mails with this warning:
We recommend renewing certificates automatically when they have a third of their total lifetime left. For Let's Encrypt's current 90-day certificates, that means renewing 30 days before expiration. See Integration Guide - Let's Encrypt for details.
What you did was correct. Certificates cannot be modified. Any change (key, domain names...) requires the issuance of a new certificate. In fact, this is also what happens when you renew a certificate - it's just a new one with same names but different expiry date.
The Let's Encrypt expiry mailer detects renewals based on the exact set of FQDNs in your certificate. If that changes, it cannot detect the renewal and will start mailing you. There is no way to avoid this, it is a limitation of how the system currently works.
You can simply ignore the emails. The mails will stop once the old certificate (with the old names) has expired.