The CMN Directory Connector can be scheduled to run at regular intervals. When running in scheduled mode, the CMN Directory Connector is not deleting contacts from the target for uses that have been removed in the source. The following note can be seen in the Sync.wlog:
The deletion was disable, enable it in advanced settings and select update all objects check box
In order for the CMN Directory Connector to delete contacts in scheduled mode, "Update All Objects" will need to be enabled on the Directory Connector scheduling screen. An existing schedule will need to be deleted and re-added for "Update all" to be set to "yes".