Your description suggests the document has acquired some of corruption. Corrupt documents can often be 'repaired' by inserting a new, empty, paragraph at the very end, copying everything except that new paragraph to a new document based on the same template (headers & footers may need to be copied separately), closing the old document and saving the new one over it.

That said, your description of what's happened with the footnotes suggests there may be more to this than just that. However, without actually seeing the problem document, it can be difficult for anyone to diagnose the issue. Can you attach a document to a post with some representative data (delete anything sensitive)? You do this via the paperclip symbol on the 'Go Advanced' tab at the bottom of this screen.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]