@Entity
public class Book extends AbstractSimpleEntity implements Serializable {
	private static final long serialVersionUID = 1L;

	@OneToMany(mappedBy = "book", cascade = CascadeType.ALL, orphanRemoval = true, fetch = FetchType.LAZY)
	@OrderColumn(name = "position")
	@Getter
	@Setter
	protected List<Page> pages = new ArrayList<>();
}

@Entity
@NoArgsConstructor(access = AccessLevel.PROTECTED)
public class Page extends AbstractSimpleEntity implements Serializable {
	private static final long serialVersionUID = 1L;

	@Getter
	@ManyToOne
	protected Book book;

	@Getter
	@Setter
	private boolean done = false;

	public Page(Book book) {
		this.book = book;
	}
}

	private static void editFirstBookPage(Long bookId) {
		EntityManager em = EmfHandler.getEM();
		try {
			em.getTransaction().begin();
			Book book = em.find(Book.class, bookId);
			em.detach(book);
			List<Page> pages = new ArrayList<>(book.getPages());

			// Uncomment this to workaround the problem
			// for (Page page : pages) {
			// em.detach(page);
			// }

			pages.get(0).setDone(true);

			Book origBook = em.find(Book.class, bookId);
			em.refresh(origBook);
			origBook.setPages(pages); // thats where done flag is reseted
			// book = em.merge(book); //Same Problem with merge
			em.flush();
			em.getTransaction().commit();
			LOG.info("Updated Pages");
		} finally {
			if (em.getTransaction().isActive())
				em.getTransaction().rollback();
			EmfHandler.disposeEM(em);
		}
	}