Generic answer: yes, each chapter can have its own header.
Header and footer are attributes of page styles.
Basically, you must create one page style per chapter. You switch from one page style to another with a specific page break, either with
More Breaks or a page break included in the definition of a paragraph style.
Since you have ~100 chapters, this is not convenient.
If your header content can be extracted from some data in the chapter (e.g. a Heading x, x usually 1, paragraph), only one page style is sufficient: the header is the value of a field insertion and automatically follows the changes across the chapters.
Working with master/sub-documents introduces an additional level of complexity. You must make sure that styles are the same in the master and sub-documents if you don’t want to be “surprised” by formatting differences. The best way to insure that is to base all files on the same template. “Templating” existing documents is very tedious and tricky, even for advanced users.
The second difficulty with master/subs is to fully understand that the styles in the master override those in the subs (this is why it is preferable to have the exact same styles in both). But variable style data is not forwarded from sub to master: this is the case for the header and even for the page style itself.
- Imagine the situation where you carefully designed a page style with header in a sub-document, whose name is the same across the collection. When the master is assembled, what should be done with the headers? To avoid this issue, the master ignores the header and uses only the one defined in the master.
- This means you must either define as many page styles in the header as including sub-docs and find a way to override the instructions given in the sub-document paragraph styles or work with the dynamic single page style through the use of fields.
Working with master/sub-documents also requires a very strict style discipline. Since your docs originated in Word, I bet they need a tremendous restyling because Word is not as strict as Writer style-wise (it has no notion of character, page, frame and list styles and proceeds heavily with what is called direct formatting in Writer).
Without information on your use of the original material, I’d recommend to merge all the files into a single document through copy/paste if you have no independent need of the parts.
To answer your question about chapter/section: a chapter is a user-concept, it usually “translates” as content between two Heading 1 paragraphs; a section is a styled portion allowing to temporarily change the characteristics/properties of a page style (except the margins and header/footer). Chapter and section do not belong in the same semantic domain.
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