If you persist or merge a versioned entity it depends on the initial version whether the *toMany collections are replaced with their persistent implementations or not.

• If the version is non-negative, the persistent implementations are in place.
• If the version is negative, the original implementations are still in place.

Hibernate handles both cases later during flush and I was not able to create a scenario where this inconsistency leads to a problem, but it is still inconsistent.

I think I've spotted the problem in AbstractSaveEventListener.performSaveOrReplicate:

if ( persister.hasCollections() ) {
	substitute = substitute || visitCollectionsBeforeSave( entity, id, values, types, source );
}

IMHO should be

if ( persister.hasCollections() ) {
	substitute = visitCollectionsBeforeSave( entity, id, values, types, source ) || substitute;
}

You may find a small stripped down test project on Github https://github.com/abenneke/sandbox/tree/master/hibernate-versions which includes a NegativeVersionTest

Thank you!