This feature of DataHub is accessible from MagicDraw's DataHub menu, see figure below.
While copying data with Sync from various data sources in DataHub, the DataHub creates DHLink to be used for synchronization. As you work with more data - the DHLink will keep building up within the DataHub project in MagicDraw® containment area. If some of these DHLink are deleted from DataHub explorer, the references will still exist within MagicDraw's project space. Clean Up DataHub Database will remove these unused references from the MagicDraw® project.
To clean up DataHub database
First select the DataHub_Data_projectname folder from the containment area.
Then click Tools > DataHub > Clean Up DataHub Database, see figure above.
If there are unused references or unused DHLink, they will be deleted. Otherwise, a message saying there is no unused DHLink will open.
The result of the clean up operation is shown in see figure below.