When Unreal autosaves, any items in the outliner from a sub-level that have been switched on by the sequencer track disappear, BUT only in the outliner, everything else can still see the scene fully (for example, the viewport is fine).
If you kick the outliner by scrubbing the timeline in sequencer for instance, then everything comes back.
Control the visibility of sub-levels by a visibility track in the sequencer.
Set the sub-levels to off by default in the persistent level and enabled by these Sequencer visibility tracks.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-164379 in the post.