In normal Smarts functionality during re-discovery of a device, existing interfaces which have an associated IP address (Underlying relationship) are selected for deletion if the interfaces are disabled on the device side. If an interface has no associated IP address, it will not be selected for automatic deletion.
These interface instances will need to be deleted manually from within the Smarts IP domain manager administrative console. To do this, right-click on the interface instance and select Delete from the menu.