@Entity
@Table(name = "ITEM",
    indexes = @Index(columnList = "CODE", unique = true))
public class Item implements Serializable
{
    private static final long serialVersionUID = 1L;

    @Id
    @GeneratedValue
    protected Long id;

    @Column
    protected String code;

    @OneToMany(mappedBy = "parent", cascade = CascadeType.ALL, orphanRemoval = true)
    protected Set<ItemRelation> lowerItemRelations = new LinkedHashSet<>();

    @OneToMany(mappedBy = "child", cascade = CascadeType.ALL, orphanRemoval = true)
    protected Set<ItemRelation> higherItemRelations = new LinkedHashSet<>();
    
    ...
}

@Entity
@Table(name = "ITEM_RELATION",
    indexes = @Index(columnList = "PARENT_ID, CHILD_ID", unique = true))
public class ItemRelation implements Serializable
{
    private static final long serialVersionUID = 1L;

    @Id
    @GeneratedValue
    protected Long id;

    @ManyToOne(optional = false)
    @JoinColumn(name = "PARENT_ID")
    private Item parent;

    @ManyToOne(optional = false)
    @JoinColumn(name = "CHILD_ID")
    private Item child;

    @Column(nullable = false, columnDefinition = "INT DEFAULT 0 NOT NULL")
    private int quantity = 1;

    ...
}

EntityManager em = emf.createEntityManager();
EntityTransaction tx = em.getTransaction();

tx.begin();

Item item = em.createQuery("select x from Item x where x.code = 'first'", Item.class).getSingleResult();

Set<ItemRelation> lowerItemRelations = item.getLowerItemRelations();
Hibernate.initialize(lowerItemRelations);

// initializing higherItemRelations prevents orphanRemoval to work on lowerItemRelations
Set<ItemRelation> higherItemRelations = item.getHigherItemRelations();
Hibernate.initialize(higherItemRelations);

lowerItemRelations.clear();

tx.commit();
em.close();