One thing I want to point out that seems to confuse a lot of people in this situation is that you will probably get a reminder e-mail from Let’s Encrypt when your old certificate is about to expire. If you replaced a certificate with a larger certificate, Let’s Encrypt does not know that one was necessarily meant as a replacement for another, as opposed to the possibility that they’re independent and perhaps being used on separate servers. In that case, an expiration warning e-mail is still generated for the smaller certificate when it’s about to expire, even though you in practice don’t need to renew it because you can simply renew the larger certificate.
You can safely ignore this renewal warning e-mail if it relates to a certificate that you are no longer using.