Perhaps this might help: today I had a similar problem, when exporting ID warned that “one or more cross-references are out of whack”.
Rather than trying to find out which one (in a four-page table of contents, referring to any of about 40 chapters spread over 8 files), I called up the Preflight Panel and checked if there was anything available for Cross Refs. Yup — there was. I made a new profile, checking only the refs, and switched it on. 1 sec. later it told me the page number of a single reference; and clicking this page number took me right to the little troublemaker.
I dunno what ID did, internally; I only had to open the corresponding referred-to file and the Preflight warning went away. Exported without a hitch, then closed the document — and then the Book panel showed a “Modified” warning! Well, I had my PDF, so I ignored that … until next time … (echoing “ha ha ha”'s in the distance).