How are you actually deleting the work items? Are you using the "Delete logically" functionality?
If a work item is logically deleted, then it cannot appear in business workplace anymore. It sounds impossible. They might be visible in UWL, if there is some refreshing problem etc. but in SBWP it really shouldn't be possible.
Which work items are you speaking about? What is their purpose? Could it be possible, that after you delete the work item, a new one is created automatically by some process?
Regards,
Karri