Try the jmx console for workflow maintenance, it gives you option to purge workflowshttp://localhost:4502/system/console/jmx/com.adobe.granite.workflow%3Atype%3DMaintenance

@robert,My bad, I confused between activate and deactivate.. if you activate a child page without activating the parent page.. you will see this kind of scenario. 

Deactivation doesn't deactivate the sub folders, so this should be expected, as you need the parent node for the sub pages.. if you deactivate the child nodes and try. i believe this shouldn't happen