Oh! I get this message for every blueprint in my level.
Currently there is only the MyCaveControllerActor one, but if I drag another blueprint in, the error is thrown for this one as well; e.g.
LogCheckComponents: Error: SerializedComponent archetype is not the CDO nor a default subobject of my class.
Me = PROTO_BP_Blueprint_0_C
/Game/Untitled.Untitled:PersistentLevel.PROTO_BP_Blueprint_2,
Component = SceneComponent
/Game/Untitled.Untitled:PersistentLevel.PROTO_BP_Blueprint_2.DefaultSceneRoot,
Archetype = SceneComponent
/Engine/Transient.PROTO_BP_B
lueprint_0_C:DefaultSceneRoot_GEN_VARIABLE