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);
    }
}

When I read in various places that hibernate didn't like you to assign to a collection, I assumed that the safest thing to do would obviously be to make it final like this:

class User {
  private final Set<Role> roles = new HashSet<>();

public void setRoles(Set<Role> roles) {
  this.roles.retainAll(roles);
  this.roles.addAll(roles);
}
}

However, this doesn't work, and you get the dreaded "no longer referenced" error, which is actually quite misleading in this case.

It turns out that hibernate calls your setRoles method AND it wants its special collection class installed here, and won't accept your collection class. This had me stumped for a LONG time, despite reading all the warnings about not assigning to your collection in your set method.

So I changed to this:

public class User {
  private Set<Role> roles = null;

  public void setRoles(Set<Role> roles) {
  if (this.roles == null) {
    this.roles = roles;
  } else {
    this.roles.retainAll(roles);
   this.roles.addAll(roles);
  }
}
}

So that on the first call, hibernate installs its special class, and on subsequent calls you can use the method yourself without wrecking everything. If you want to use your class as a bean, you probably need a working setter, and this at least seems to work.