Certain changes to a document may require you to manually instruct Affinity to update cross-references' values.
Preflight will generate errors for any cross-reference that is out of date or invalid after you:
When a document is a book chapter and contains cross-references to other book chapters, ensure the book is open on the Books panel before updating cross-references.
The Books panel's Preferences menu includes options to update cross-references: in all of the current book's chapters immediately, and when outputting (exporting or printing) books.
On the Cross-References panel: