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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a book file from InDesign to PDF (and maybe other formats) it is possible to get an error message, "Unresolved or out of date cross-references" followed by a list of documents with that problem.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markers, and any stray single markers, should appear in the "Cross-References" panel, with a flag if invalid or out of date.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?

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It may be possible to fix this instantly if one is familiar with InDesign scripts, but maybe not because there are many complaints in the Adobe forums.

After two days of struggle, I found an inelegant and time-consuming but effective way to find and fix these. I'm posting in case there's not a better way. (And, if there is, please answer my question to help others.)

  1. Save your InDesign file as an IDML file.
  2. Rename the file, changing the extension from idml to zip.
  3. Open the zip file and the Stories directory that's inside it. Copy all the stories.
  4. Paste the stories in a directory you created for that purpose; you'll delete it later.
  5. Use the operating system's search function to find which of the story files contain the text of your document by searching the directory for a phrase in your document.
  6. Check those files and find the one that contains <CrossReferenceSource I used Notepad++ for this.
  7. Search, using your editor's search function, for each instance of <CrossReferenceSource and examine the <content> element. You are looking for things that do not appear in the Cross-References panel in InDesign. Here's one: Screenshot of XML showing bogus cross-reference The supposed cross reference is the string "n in".
  8. You will be able to see the surrounding text in the XML. Use InDesign's search to find that place in your document.
  9. Open the story editor. It will be positioned near the area you just found by searching. Cross-reference marks are blue rectangles with pointy triangular ends. (Picture below.) Find the bogus cross reference.
  10. Copy a few words before the bogus cross-reference, the opening cross-reference, and the contents, but not the closing mark. Screenshot of finding a cross-reference in story editor, showing what to copy
  11. Leaving the copied text highlighted in the story editor, paste what you just copied into a plain text editor. I used TextPad. The idea is to strip out that cross-reference mark.
  12. Copy the text from the plain text editor and paste it into the already-selected space in the story editor. Both cross-reference marks will disappear. Close the story editor so it will re-position if you find another one.
  13. Repeat as needed until you've found all of them, then save and close your InDesign file. Erase the zip file and the directory you made to hold the story files.

I hope this helps someone!

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