I am using a certificate with my WCF service so have an encoded value in the web.Config
This can be done by exporting the certificate (via IIS or Certificate Snap In) to a .cer file without the private key in base64 form, then opening in notepad and copying and pasting this into encodedValue
If it's managed by a 3rd party then the server certificate is going to be loaded into the Windows certificate store and selected as part of the service behaviour
In the service behaviour you can select the certificate it uses on the endpoint by
<behaviors>
<serviceBehaviors>
<behavior name="MyServiceBehavior">
<serviceCredentials>
<serviceCertificate findValue="CN=myhost.mydomain.org" />
</serviceCredentials>
</behavior>
</serviceBehaviors>
</behaviors>
The element is used for a connecting client. Simply refresh the service reference for the proxy in the client solution and the identity element should be updated with an encoded value version of the public parts of the new certificate.