Markup structure has to become a fixed page layout
XHTML describes document structure; PDF describes pages. Headings, lists, links, and tables may be laid out according to available styling and rendering support. A screen-oriented stylesheet may not produce sensible paper dimensions without print-specific rules.
The PDF is useful when readers need a portable document, but it does not keep the source markup equally convenient to edit. Retain the XHTML and related resources if the document will be revised or published again.