On deleting an object from the old repository version, create the Object Deletion object in the update. The object will be deleted on update.
NOTE. Adding an object deletion is available only in the desktop application.
To add an object deletion to update:
On the Repository tab select the Add Object Deletion to Update context menu item for the selected object.
On the Update panel select the Add Object Deletion context menu item. Specify the object to be deleted in the dialog box that opens.
Using the 
button on the Update panel. Click the button, select the Delete Object item in the drop-down menu and specify the object to be deleted.
In the update structure a deletion object is displayed as an icon with red cross:
NOTE. On separating administrator roles the object deletion cannot be added using security administrator permissions.
See also:
Creating an Update | Adding Comments to Update