Importing a second Index from Word 2010 into InDesign CC

I am working on a 1000 page book. It was imported from Word 2010. Things imported messy but I am cleaning it up. The second index imported as text but did not attach to the reference in the text. The Index worked as did the table of contents. What can I do and how do I work with this. I have never had this kind of a situation.
Thanks

Make sure to open the track changes dialog and accept the changes, then do a Save As to rewrite the file.

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