Track Changes usually causes the footnote numbering to be 'wrong', not to 'restart'. If you have tracked deletions in the sequence, then the remaining footnotes are numbered too high, because the tracked deletions have not yet been physically removed from the file.
In which case, the numbering will come right when you accept all changes. I don't think that's your problem here. The footnotes are a 'list'.
How to remove all footnotes quickly in Word? Footnotes are used for detail comments in printed documents, and it consists of two parts- the note reference mark and the corresponding note text. Microsoft Office Word always places footnotes at the end of each page.
Either one list on each page, or one list for the entire document. If they are set to 'Restart Each Page' and you add a new one to a page that doesn't have any, then you will indeed get a note numbered '1'. But in that case, the original footnote on that page will now be numbered '2'. What I suspect has happened is that someone has opened that file in one of the other applications out there that impersonate Word, such as LibreOffice. That will have converted the footnotes to text, so you will have to re-insert them ALL.
Immediately beside each old footnote, insert a new footnote. Copy the text of the old footnote to the new footnote, then delete the old. When you get to the end of the document, your numbering should be correct (if it isn't, you've missed a few.) Hope this helps John McGhie, Microsoft MVP (Mac Word), Consultant Technical Writer.