Update the book, N.
> Starting from a .book file ...
I recommend setting the numbering properties from within each open component file, then setting the book menu clones to "Read from File".
And I concur that you may see no changes until Update Book.
For what it is worth, I have never had a problem setting the numbering from the book file. I find it easier than setting each file within the file.
It only causes us a problem when FM (7.1/Unix) crashes, which, alas, it does, a lot.
And because unexplained crashes seem to still be an undocumented feature, even in FM11, the risk of book/file numbering de-sync might still lurk.
But for anyone who is not experiencing frequent crashes, setting props from Book might be just fine.
I always recommend setting the numbering at the book level as sometimes files can be common to multiple books and their position within a book would be different in each book. The book settings always trump the file settings anyway and you have easier control over the book's collection of files that way. If I have to rearrange files in a book.
In FM10 and later, one can turn off FM's error/warning notifications, so in some cases when the book has to silently open files to perform the updates, you won't see the errors/warnings (like missing fonts or inconsistent properties) that can stop FM from automatically completing the renumbering of a book.
Also, when changing the setting for a single file in a book, the status line in the book pane doesn't automatically update until you come back to the file (i.e. select another file and the re-select the file that you just updated). This might be what you're seeing and I think it's a "buglet".
OK, I'm reassured … I'll mentally label this quirk 'delayed feedback', especially now I've started the day by opening the book and see that numbering is as I'd hoped.