calibre stores tempfiles on Windows in "%TEMP%" (which should equate to "%USERPROFILE%\AppData\Temp"), or on unix, "$tmp" ("/tmp").

They will be in folders titled "calibre" with a random string appended.
Not sure how much that will help you, since anything it creates will be in the output you already created, and you cannot really pause say a conversion while you replace stuff... but yo can certainly take a look at what gets created there.
If you want to replace the ToC.xhtml, you *can* always just use Edit Book...