If your Express (Node.Js?) server isn't using the newly renewed certificate, this can be due to a few things:
Perhaps Express isn't configured properly, so it points to a certificate file which wasn't updated when your certificate was renewed;
Perhaps you just need to reload your Express server, so it loads the renewed certificate, if it's properly configured.
Note that as @JuergenAuer already said: certificates are port agnostic, they are only coupled to hostnames. So you don't require separate certificates for different ports!
Also, you've got three Let's Encrypt certificates from March 20th. If the issuance of the certificate was without problems, but the installation isn't done properly, it doesn't help to keep re-issuing new certificates, as the problem was not with the issuance in the first place, but a step in the process afterwards. Please don't re-issue certificates if the problem is with the installation of the certificate.