Here's a weird one: updating a book with Frame 2015 (18.104.22.1685); the doc has several settings of conditional visibility, plus a couple of imported mifs that are also conditionally visible. While updating, I got an unresolved cross-reference error out of one chapter. The link in the error file went to the first page of that chapter, not to the erroneous cross-reference. Searching for unresolved cross-references produced no results, in the body or master pages. I set the conditional visibility for that chapter to "show all" and updated the book again. I got the expected errors for inconsistent show/hide, but no errors for unresolved cross-reference. I set the show/hide back to the correct settings, updated the book again, and got no errors.
This solution scares me - what do I do if it doesn't work? Is there a better answer?
Were all of the files open in the book when you did the book update? If there was an error opening a file during an update, e.g. a missing font, then that would also create a broken cross-ref message, as that file couldn't be opened for the update.