It appears that you get to run OCS forest prep again:
From Office Communications Server 2007 Document: Supportability Guide:
http://www.microsoft.com/downloads/details.aspx?FamilyID=f8cc9b59-225f-425d-bd3a-e506396c6207&DisplayLang=en
"If you have an existing Windows Server 2003 forest running Office Communications Server, and upgrade any of its domain controllers to Windows Server 2008, Office Communications Server will not work correctly; some UI elements will disappear, and you will be unable to add more Office Communication Server servers or pools. To resolve this issue, you simply reissue the command to prep the Active Directory forest for Office Communications Server.
To do so using the user interface, use the Prep Forest option of the deployment tool (for more information, see “Running Prep Forest” in the Microsoft Office Communications Server 2007 Active Directory Guide)."
