Hi,
> and then I paste in paragraph-by-paragraph into a copy of the blank 
> document,
> save it, and re-generate the TOC. It takes hours, and seems ridiculous 
> compared
> to the five seconds it requires to regenerate a LaTeX document, but I 
> really have no choice.
Using styles consistently throughout a document, usually ensures a 
stable/robust document. It is not necessary to copy content into a new 
document, especially not to copy "paragraph by paragraph".
If a document is really damaged, you have to paste content as “unformatted 
text” into a new document.
I guess, the problems with your document are not caused by styles, but by 
other issues.
-- 
Cheers,
Lisa