In some circumstances a certificate that is installed on a Lync Server may now show up on the Certificate Wizard, we are going to troubleshoot and find the root cause of the issue.
I had this issue this morning, when a new certificate was issued on the Internal PKI, however before getting to that point the customer asked me to identify why a new certificate that was requested using the Certificate Wizard was not showing up.
My first step was to check the Certificates using MMC, and as we can see we have three entries (The Public Certificate, the old and the new Internal Certificate), by the way this server was a Lync Edge server.
The second step was trying to assign the certificate however the list of certificates had only two certs instead of three.
Time to go back to the MMC, and check the certificates individually and during that task, we found out that because of the internal PKI changes the cert was no longer valid. The solution was to make sure that the certificate chain was in place in the current server, and as soon as the certificate showed as valid, then it started showing up on the Lync Certificate Management.
The issue hasn’t happened internally because the GPOs took care of the new PKI certificates to the clients, however the same thing does not happen on member servers and especially in servers located in the DMZ.
So, lesson of the day, having issues with mysterious certificates not showing up on the Certificate Wizard, check if they are still valid and a good start is to make sure that your PKI has all the certificates in place on the member servers.