I have the same issue. I really wonder why this issue hasn't come up earlier with more attention as having an ElementCollection in an Embeddable doesn't sound to be an exotic use case. Attention: this is not related having a nestedn ElementCollection in another ElementCollection.

Digging into the code I found the causing issue in the TypeHelper.class in Line 240. The recursive call has no effect at all, as it just copies the values into a new Object array, but doesn't process the result. A quick test showed that the issue can be fixed by applying the result values to the containing object:

Object[] values = replaceAssociations(origComponentValues, targetComponentValues, subtypes, session, (Object) null, copyCache, foreignKeyDirection);
componentType.setPropertyValues(target[i], values, null);

hibernate-test-case-templates.zip