If you're using the Layout > Table of Contents menu, you'll be picking entries entirely based on paragraph styles. The entries will be formatted by paragraph styles. After doing that, when you're ready to have new pagination, choose Update > Table of Contents and it will use the same paragraph styles.
@Ariel, your reply was blank.
I was just saying:
I understood that the OP is talking about an own-formatted TOC (there
was a typo in the OP, but that's what I understand): i.e., a TOC in
their book that they've extensively formatted beyond what is achievable
through the very limited built-in TOC feature.
In such a case, where all the formatting in the TOC will be lost if the
TOC is updated, I recommend my script, LiveTOC (it's the only one I know
that does this), that effectively turns the pages numbers in the TOC
into hyperlinks, so that they update automatically if the pagination