@Entity
@Table(name="items")
public class Item {

    ...other fields...

    @ManyToMany(fetch = FetchType.EAGER)
    @JoinTable(name = "items_tags", joinColumns = @JoinColumn(name = "item", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "tag", referencedColumnName = "id"))
private List<Tag> tags = new ArrayList<>();

}

public void deleteTags(List<Tag> selectedTags) {
    for (Tag tag : selectedTags) {
        em.remove(em.merge(tag));
        }
    }

@EJB
private ItemsServices is;

@PersistenceContext
private EntityManager em;

...stuff...

public void deleteTags(List<Tag> selectedTags) {
    List<Item> items = is.getItems();

        for (Tag tag : selectedTags) {
            for (Item i : items) {
                if(i.getTags().contains(tag)) {
                    // Do some popup
                } else {
                   em.remove(em.merge(tag));
                }
            }
       }
 }