Fixed in the next release. Editing a page is supposed to recalculate the location in the book based on the "new" previous chapter's location, in case the current page's location was changed by the edit, or in case the location record was missing for some reason.
However, there was a bug doing this when editing the first chapter in a book:
In this case, the "previous" page in the book is the book intro. Normally, when you have a sibling chapter with subchapters, followed by the current chapter, you would want the current chapter to appear after all the previous chapter's subchapters. But since a parent book was being confused here, its sub-chapters are actually the chapters in the current book (so the first chapter appearance was changed to the end of the book).
Once the first chapter in the book was messed up, things got weird. Editing the other chapters in the book could also get pushed to the end, because they knew they were supposed to appear "after" certain other chapters and the intended order had not been changed.
Since the underlying issue of the first chapter confusing the parent book with a sibling book is now fixed, there would be two ways to correct the TOC:
- As you found, change a value in the Manage Chapters tab, which recalculates the whole book, OR
- Edit the affected chapters one by one, in order, starting with the desired first chapter. Since each chapter jumps to be after its specified previous chapter whenever you edit it, eventually the order should correct itself. Once the order is correct, future edits should have no effect on the order.
The bug first appeared in 4.0.0 Gamma 4, from 2014.