Exchange Server – How to use existing certificate without CSR

Apart from the required internal FQDN's and server names, you only need the domains on your certificate that you need to securely access your server on (OWA or ActiveSync for example). Your Exchange server can accept mail for any number of other domains, but if you only access OWA on mail.acme-widgets.com then that is the only external DNS name that needs to be on the certificate.

As an example, our Exchange server accepts mail for about 30 domains, but we only have the following things on our certificate (pardon the whole Acme Widgets thing, but you get the idea).

svr03                               (Internal server name)
mail.acme-widgets.com               (OWA domain)
autodiscover.corp.acme-widgets.com  (AutoDiscover internal FQDN)
autodiscover.acme-widgets.com       (AutoDiscover external FQDN)
legacy.acme-widgets.com             (Legacy domain)
svr03.corp.acme-widgets.com         (Internal FQDN)

If I recall correctly, when I was going through the Exchange certificate wizard it did include all of our auxiliary domains, but I chose to remove them. It shouldn't hurt to leave them on, and if the certificate wizard includes them by default, it's certainly not wrong to leave them.

There is no problem at all in using the same certificate in two different applications, if everything else is ok. The certificate in itself is not the problem, the problem lies in some misconfiguration on the Lync side.

You should check all URLs Lync uses (they are a lot...), and verify that your certificate actually contains all the names being used. Also, you should check everything else... DNS, firewalls, FQDNs, updates, event logs... there are literally tons of things that can go wrong when setting up Lync, and can have side effects ranging from "quite understandable" to "totally crazy".