A user in my office must mark entries for Table of Contents. Is there any
way to mark entries, but keep the automatic numbering which was applied to
that paragraph?

This user is doing it this way as opposed to using headings/styles as there
is some Collaboration on the document, and most paragraphs have been marked
(by the other office) as a style with a custom heading 2 (for the second
level), and all paragraphs cannot be included in a generated table of
contents, and we cannot change the styles applied to the paragraphs as the
document will be send back to their office.

Thank you.