This is actually a bug and is fixed for the next build.
What happens is this:
If the level 2 book already contains all its chapters, and is added to a higher level book, some code that was added to simplify a database query (removing the lower-level book itself from the query) actually prevents the chapters in the lower-level book from being associated with the top-level book as well. This has been fixed by changing the index used by the WHERE condition.
The upgrade script should fix any chapters that are broken in this way.