This is an edge case that can also be caused when a Level only contains actors were `SupportsExternalPackaging` is false. This is likely the case for the "empty" level which surely contains a LevelScriptActor.
MapCheck: Error: Level Instance /Game/NewMap.EmptyLevel is not using external actors, resave level to add compatibility /Game/EmptyLevel.EmptyLevel
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-353000 in the post.