After digging into the issue and the error I found that I will have to restart the Active Directory Certificate Services on CA server. Looked into application log and found the event id 53.
I checked and found that Active Directory Certificate Services service on CA server service is already running.
Now I just had to restart Active Directory Certificate Services service. After restarting the service, request the certificates again from Lync server and it will complete successfully.
Cheers,
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