The hierarchy of a LevelInstance actors (Outliner) will break when cooking.
The source is the call to AActor::RerunConstructionScripts in FWorldPartitionLevelHelper::MoveExternalActorsToLevel. The construction script destroys the BPs component and recreates them. This is the Parent in the current scenario. The Child is referencing its Parent's RootComponent as its AttachParent. That reference becomes invalid because of the CS and the usual code that fixes those reference relies on the AttachChildren of the Parent. Filling the AttachChildren relies on the Actor\Component being Registered which does not happen when cooking. The invalid reference is discarded by the validation code at the end MoveExternalActorsToLevel.