Updating TOC erases all document text

Hello all. I am working with a document in cs4 that I placed in from Word. All the heading styles were set in InDesign. There are graphics and text. I inserted a TOC on the first page early on. I then went to Update the TOC, and it asked if I wanted to include overset text. I clicked yes, and then all text in the entire document disappeared and was replaced by a TOC that only listed the very first heading of the document. Any time I try to insert a new TOC or update the TOC, this happens. What might be going wrong? I'm relatively new at making TOC in InDesign/working  with large documents, and just completely baffled. Sorry if this is a very simple fix. Thanks.
Edit to add: I have also re-set my preferences and this did not solve the problem.

Your TOC must ALWAYS be a separate story that is not threaded with any other text.

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