Hi SPDT13,
I don't know of any option to edit the TOC
during conversion instead of at the end of it.
But you can flatten the TOC of any AZW3 or EPUB book
before conversion by calling the
Edit TOC feature separately.
This tutorial show you how to add the
Edit TOC button to your toolbar, if necessary:
http://blog.calibre-ebook.com/2013/0...r-e-books.html
This tutorial show you how to flatten a TOC (simply scroll past the first part which explain how to create a TOC):
http://blog.calibre-ebook.com/2013/0...e-toc-for.html
Does that help
?