It sounds to me there is a pretty good likely that you'll need to do some common troubleshooting.
Your InDesign file might have become corrupted. It that case save it as an IDML file. See this tutorial: http://www.pfl.com/cidf
Or you may need to restore your InDesign preferences. Described here: http://pfl.com/trb
I'm having the same issue but I've sort of figured it out. When the MS Word file was imported it had funky cross references in it. We later found that the author was using some kind of third party application/plug-in to manage his end notes (cross references). So after the document was imported we continued to work away at the layout and design not realizing that it was full of these broken cross references. We have finished the 200 page document and now want to export to html, ePub and PDF. When exporting the PDF we get the un resolved error but the PDF exports fine after accepting the error window. Exporting ePub and HTML crashes InDesign.
So here's what I found. When you go into Story Editor mode you can see all the cross references through out the document. Thousands in my case. So even though the cross references panel shows nothing there are indeed cross references through out the entire story. What I don't know how to do, is easily remove these cross references. I can manualy go through the story in Story Editor and retype the affected text but that is going to take a long time in my case. If any one knows how to do this quickly it would be greatly appreciated.
So gscortino1, I recomend going into Story Editor mode and seeing if you can find a funky cross reference and remove it. Then try to export your document.
I'm actually realizing now that they are not funky cross referenes but rather funky hyperlinks. I'm still stuck on how to clear them quickly.
Learning a little more about the problem.
All my text resides in icml (InCopy Markup Language) files so it allows me to easily see what's going on by opening the file in dreamweaver.
Using dreamweavers find function I located some of the problem hyperlinked text areas and compared them to none problem hyperlinked text areas.
Here is what I have found.
The good areas have the following information associated with them:
<HyperlinkURLDestination Self="HyperlinkURLDestination/www.iaea.org/About/Policy/Board" DestinationUniqueKey="4098" Name="www.iaea.org/About/Policy/Board" DestinationURL="www.iaea.org/About/Policy/Board" Hidden="false"/>
<Hyperlink Self="u43e09" Name="Hyperlink 2" Source="u4385f" Visible="false" Highlight="None" Width="Thin" BorderStyle="Solid" Hidden="false" DestinationUniqueKey="4098">
<HyperlinkTextSource Self="u4385f" Name="Hyperlink 644" Hidden="false" AppliedCharacterStyle="n">
If you notice, the <HyperlinkTextSource> tag has a setting called "Self". This appears to be linked to the <Hyperlink> tag "Source" setting. And finally the <Hyperlink> tag is linked to the <HyperlinkURLDestination> tag through the "DestinationUniqueKey" setting.
The bad areas are missing matching <Hyperlink> <HyperlinkURLDestination> tags:
<HyperlinkTextSource Self="u437f4" Name="Hyperlink 17" Hidden="false" AppliedCharacterStyle="n">
<Content>UN, 2011c: 15</Content>
So if I can figure out a way to generate the needed <Hyperlink> <HyperlinkURLDestination> tags or delete the surrounding <HyperlinkTextSource> tags, I should be good to go.
I think I found my issue with the help of my fellow writers. Word as usual is full of "Extra Features" and one of them is when you import a word doc into indesign it loads up " Hyperlinks" in the Character styles. These were the hypelinks that were out of date as soon as I deleted them the issue when away. Thanks to all.
What does a cross reference look like in story editor? Is there a special symbol?