Currently parent blueprints are added to the list of blueprints to nativize if their children are flagged to be nativized only if they are also individually saved.
Ideally, we'd update the list of blueprints for nativization with the parent when the child itself is saved to prevent problems from arising when saving only the child blueprint. (I.e. user may flag child for nativization, then save it and close out of the editor while not wanting the other changes they've made throughout the session and therefore not saving the other assets on close.)
Found on //UE4/Release-4.15 CL-3269047
Result: Only the child blueprint has been added to the array for nativization.
Ideal: On save we update the array with the entire list of those waiting to be added (i.e. the parent as well.)
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-41071 in the post.