That is the issue, there is currently an open defect on this. Here are the details I can provide:
Problem
The directory server information (eg. IP address, machine name, or port) has been modified. Imported organizational units (OUs) no longer synchronize.
Solution
When changing Directory Server information within the Endpoint Manager (SEPM) to match a modified directory server's configuration the Endpoint Manager appears to accept the change; however, further attempts to synchronize Organizational Units imported from that server fail. As a work-around delete the Directory Server from the list in the SEPM then add it again with the new information. Any organizational units imported from this server will also need to be removed, re-added, and have their policies reassigned.
This is scheduled to be fixed at some point, ETA is unknown however. Hope this helps a little.