A PDF file is not a source file. When we work from a pdf, we export the pdf to a workable .doc file. This deconstruction process is not perfect and does not accurately translate formatting and break paragraphs where they shouldn't be.
In order to maintain the integrity of the intended format, we have to manually go through the PDF file paragraph by paragraph and make changes in the source file. As you can imagine, this is time consuming and prone to human error.
Ideal source files are Microsoft Word, Open Office, or Apple's iWork Pages.