So today I was publishing the Lync topology into SQL and tried using a DNS alias to our SQL server(s). No go, however it built my Central Management Store and put the DNS alias into Active Directory. No matter what I did I could not republish a new topology with a different SQL CMS location as this was stored somewhere in AD. I found a simple PowerShell cmdlet that comes with Lync, Remove-CsConfigurationStoreLocation. Rather than going into ADSIEdit, I took a swing at this option. I ran the following with no parameters and it cleared everything up and I was able to republish.
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