When one exports a book file from InDesign to PDF (and maybe other formats) it is possible to get an error message, "Unresolved or out of date cross-references" followed by a list of documents with that problem. This problem doesn't show up in, with a pre-flight.
Sometimes you can find the problematic cross-references in the Cross-Reference panel or the Hyperlinks panel, but not always. They do show up on Story Editor as cross-reference markers enclosing something that's not a target for a cross-reference. You can strain your eyes looking for those, and it's easy to scroll by them.
So, how can I find and fix these?
Rant: Every pair of cross-reference markers, and any stray single markers, should appear in the "Cross-References" panel, with a flag if invalid or out of date. Are you listening, Adobe?