Track Changes in documents with fields, footnotes, paragraph #s, etc. always present problems until the changes are accepted/rejected. There is simply no means of a TOC, for example, reflecting a potentially deleted heading that may or may not have been potentially replaced by another one or has had a new entry added before it. Depending on your requirements, you might try turning off Track Changes while updating the TOC.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]