Normally, an upgrade Cisco CallManager has no effect on the corporate directory, so and unknown issue has occurred.
In this case, the users listed in the corporate directory were not in the default Organizational Unit (OU). The Cisco CallManager administrator had created a custom OU for the users. During upgrades only the default OU is transferred over to the new version, and that container is OU=USER. The resolution of the issue is to transfer the list of users manually, rather than relying on the Cisco CallManager installation scripts to handle the action.