Reported behavior:
Given Level_A which contains object_X, where object_X references Level_B
Initial report indicates that `LOAD_EditorOnly` flag is absent when loading the map for the soft reference instigated by FAssetRenameManager::LoadReferencingPackages. A workaround was provided whereby simply unloading the level if it was found not to have references requiring a fixup. This workaround appears to have protected against the potential for data corruption, but a solid repro and further investigation into a proper fix is necessary.
See UDN thread for additional details.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-61910 in the post.