I don't know exactly what is causing the problem, but I can definitely see it in Story Editor.
In the screen cap below, the story editor windows on the top row are your file, and the bottom row are a new file with your text pasted in and new cross-ref added. Note the differnce in the tags:
I cant find any casue for the difference, and I don't know what the defective tag is all about. I thought perhaps it was related to a third-party x-ref plugin, but I don't see any sign of that, either. I'm stumped, and the pragmatist in my says copy and paste and move on for now, but save a copy for further exploratin when you have time.
And ask the other agency to tell you what they did and if they use any third party plugins.
A pretty weird case. The <pageNum /> building block is broken and does not display any text! (As well as <paraNum /> -- the others *appear* to work.)
Open as copy and export to IDML -- the common fixes -- don't seem to do anything useful. In addition, examining the IDML does not reveal anything different. Opening the IDML in CS4 doesn't work either, it's also broken in there. Copying the text frames to a new document invalidate the cross-references, so you have to rebuild them from scratch.
Nothing else I can think of ...
The deadline for the project is fast approaching so I have had to resort to manually adding the cross references (even though I know it will be a nightmare when I put the individuals files together as a book).
The only fix to the problem I have found is to create a new document and copy the text into the new document.
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for those that are interested, I found a solution to the issue.
What I did was create a new document using and used the 'Move pages" feature to transfer all the pages from the currupted ducument to the new indesign document. Once I did this the cross references worked immediately.
I am sure there will be other solutions but this is the only one that has come up so far.
Thanks for your responses.