I’ve put together a longish project which I compiled as a Word 2010 document. But a curious glitch emerged. When I try to add new footnotes, Word would not automatically update the footnote numbering. I end up with, let’s say, footnote no.12 followed by footnote no. 3 and so on.
I prefer doing the final editing directly into the compiled Word document because I find Scrivener’s footnoting a bit cumbersome. The subject is such that it needs updating until the very last moment before submitting the manuscript – and that means footnotes removed and footnotes added until 5 minutes to 12.
Any ideas will be greatly appreciated because my deadline is March 30.
This isn’t necessarily a problem, as long as you can manually update all your fields successfully (footnote numbers, table references, etc.)
In your Word document, press Ctrl-A to select the entire contents, then press F9. Depending on the length of the document, this may take a minute – but every reference (table of contents, table fields, references, footnotes, etc.) should be updated and made sequential.
If that doesn’t solve the problem you see right now, you may have a corrupted Word doc.
Many thanks! Will try pronto!!! 
I’m having the same problem, and the proposed solution isn’t working for me. It is not updating. Any other options?
If your problem is in the compiled Word document, and the footnote numbers are all actually fields and not just regular text, and Ctrl-A then F9 is not working to update the fields, you probably need to pursue help via Microsoft’s forums/support options.
I solved this by converting to .doc rather than .docx, but it seems to be a bug in the conversion to dotx.