If you set the deletion indicator for an item, the item remains in the document but cannot be processed. This will unblock the material.
If you delete a document, it is physically deleted if there are no inventory difference postings for its items. If a difference has been posted (for your scenario), the document is proof of the posting. Therefore, it is simply flagged for deletion. This means it can then be displayed, but no longer processed. The document is physically deleted when the next reorganization program is run.