When a Sub Level is currently open (meaning it is listed as the persistent level in the levels window) and you save the level using the levels window the map build data registry will get destroyed.
This will cause an error when you open the persistent level using that sublevel.
Map Build Data Registry gets destroyed.
Map Build Data Registry remains intact.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-44197 in the post.