If you create and persist a new entity in onFlush, then calling EntityManager#persist() is not enough. You have to execute an additional call to $unitOfWork->computeChangeSet($classMetadata, $entity).
Changing primitive fields or associations requires you to explicitly trigger a re-computation of the changeset of the affected entity. This can be done by calling $unitOfWork->recomputeSingleEntityChangeSet($classMetadata, $entity).