Hi Drew,
If it is only minor changes, then editing the LYNC Configuration within Prognosis is the best option.
If there are major changes, removing and re-adding the Lync Site using Auto-Discovery mechanism (Pointing the wizard to the new CMS server) might be a better solution.
If you are unsure which path to take, you can generate the TBXML from the Topology Builder and log a quick case with that and an irfax from the monitoring node and support can review it and give you advice. We are happy to assist but in this case, it might be best doing it via a support case so you can provide supporting diagnostics to help us give you the best advice.