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You will need to update the Cross-Refernces inside the documents.
Open Book in Indesign than go to the book panel menu to update the all cross-references. Because you have created the cross-references before separating the document into Multiple files Indesign might not be able to update the cross-references but at least it will show all the documents which have cross-reference Errors. You will have to manually correct each of the references.
To find all the cross-reference errors in the file..open the file and go to window > Type & Tables > choose Cross-References... it will show the errors with the question mark on red flag. Double click to edit the cross-references and change the document to choose the document from which you want to cross-reference.
Some Screenshot for help -
Thanks so much, that was really helpful for the cross-references. Is there a similar process for updating the Table of Contents (TOC) and bookmarks which now span multiple documents within the book?
I see now that I need to check the box (after showing More Options) to Include Book Documents within Table of Contents. Cheers