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

Check all of the places where you are assigning something to sonEntities. The link you referenced distinctly points out creating a new HashSet but you can have this error anytime you reassign the set. For example:

public void setChildren(Set<SonEntity> aSet)
{
    this.sonEntities = aSet; //This will override the set that Hibernate is tracking.
}

Usually you want to only "new" the set once in a constructor. Any time you want to add or delete something to the list you have to modify the contents of the list instead of assigning a new list.

To add children:

public void addChild(SonEntity aSon)
{
    this.sonEntities.add(aSon);
}

To remove children:

public void removeChild(SonEntity aSon)
{
    this.sonEntities.remove(aSon);
}

The method:

public void setChildren(Set<SonEntity> aSet) {
    this.sonEntities = aSet;
}

works if the parentEntity is detached and again if we update it.
But if the entity is not detached from per context, (i.e. find and update operations are in the same transaction) the below method works.

public void setChildren(Set<SonEntity> aSet) {
    //this.sonEntities = aSet; //This will override the set that Hibernate is tracking.
    this.sonEntities.clear();
    if (aSet != null) {
        this.sonEntities.addAll(aSet);
    }
}