What is happening is that Hibernate requires complete ownership of the children collection in the parent object. If you set it to a new object, Hibernate is unable to track changes to that collection and thus has no idea how to apply the cascading persistence to your objects.

So the code like:

this.children = someNewSetOfChildren;

or like:

parent.setChildren(someNewSetOfChildren);

results in a HibernateException with the message:

A collection with cascade=”all-delete-orphan” was no longer referenced by the owning entity instance

The full stack trace of the exception is:

org.hibernate.HibernateException:
A collection with cascade="all-delete-orphan" was no longer referenced by the owning entity instance: entities.Parent.childs
    at org.hibernate.engine.internal.Collections.processDereferencedCollection(Collections.java:116)
    at org.hibernate.engine.internal.Collections.processUnreachableCollection(Collections.java:67)
    at org.hibernate.event.internal.AbstractFlushingEventListener.flushCollections(AbstractFlushingEventListener.java:245)
    at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:100)
    at org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:55)
    at org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1099)
    at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1528)
    at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:374)
    at org.hibernate.internal.CriteriaImpl.uniqueResult(CriteriaImpl.java:396)
    ...

To avoid this problem, any time we want to add or delete something to the list, we have to modify the contents of the collection instead of assigning a new one with code like:

parent.getChildren().clear();
parent.getChildren().addAll(someNewSetOfChildren);

or like:

public void setChildren(Set<Child> someNewSetOfChildren) {
 
    //
    // This will override the set that Hibernate is tracking.
    // this.children = someNewSetOfChildren;
 
    this.children.clear();
    this.children.addAll(someNewSetOfChildren);
}