When you're using Author, its focus affects where objects are stored.
When adding objects directly to a folder, the focus is not an issue because you're in the correct folder by default.
When you create new objects or add new objects to a book, they will be stored in the folder that is currently "in focus". If you've specifically selected a folder in the Folders pane, that is the folder in focus.
However, if you didn't choose a specific folder before adding content to a book, the focus may be on a folder that was previously selected, which may not be the folder containing the parent, or the object being modified. Check to be sure your changes were made in the correct folder.
If you added objects to the wrong folder, you can easily move them.