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@lance_7340 -- You could try to fix it in the IDML file. Not just a simple roundtrip, but a fix. It's more straightforward than it looks.
1. Export the document to IDML.
2. An IDML file is in fact a ZIP file. Unpack the file. If necessary change the IDML file type to ZIP. You'll see six folders and two files:
3. Open designmap.xml and look for the <Index> section. The section looks as follows (this sample document contains just two topics, Azerty and Qwerty; Azerty has a cross-reference to Qwerty):
<Index Self="uff">
<Topic Self="uffTopicnAzerty" SortOrder="" Name="Azerty">
<CrossReference Self="u11d" ReferencedTopic="uffTopicnQwerty" CrossReferenceType="See" CustomTypeString="" />
</Topic>
<Topic Self="uffTopicnQwerty" SortOrder="" Name="Qwerty" />
</Index>
Now, I don't know what that section in your file looks like but you should be able to identify the topics with missing cross-references. How you proceed now depends on how many cross-references there are and how many of them are faulty. If there are only a handful of ill-formed items, delete them and redo them in InDesign. If that turns out not to work, delete all the lines that start with <CrossReference .
4. When you're done, save designmap.xml and zip up the files in the folder. Change the ZIP file type to IMDL and open the IDML file in InDesign. Check the state of the Index panel.
Hope this helps. I can't reproduce the problem so I've no idea whether the above works. As I mentioned earlier, if you can post your file somewhere (or the exported IDML, which will be much smaller than the 340 Mb file) I'll happily take a look.
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