I came across this bug when updating a project for a customer.

The code uses merge() to persist new entities.
It then calls flush() to get the generated PK and tries to insert different entities, I have reproduced the problem with a simple parent-child relationship.

When merging a parent-child, one-to-many relationship with cascade-all and orphan-removal true, the following HibernateException is thrown:

org.springframework.orm.hibernate5.HibernateSystemException: Don't change the reference to a collection with delete-orphan enabled

A full project is attached but here is the code which causes the problem:

{{Parent p = new Parent();

p.addChild(new Child());
p.addChild(new Child());

getHibernateTemplate().merge(p);
getHibernateTemplate().flush();}}

The exception is thrown when the transaction is committed when the method returns but I believe it will occur if flush() is called twice at the time the second one is called.

If flush() is not called, the transaction completes successfully.