Scanning incomplete and updated documents

I recently received a bunch of hardware/software documents to scan. I am only roughly familiar with the systems covered by the docs. I have encountered a couple situations that I would like guidance on. 1. One document is a software installation manual in a loose leaf binder with other documents. It has a title page, tables of contents, etc., several chapters, and then it gets interesting. It has several appendix sections (starting at A), an index, then more appendix sections (starting at A as well), and then another index. The document title and its font match of the second set of appendix sections and second index matches the table of contents and chapters. The first set of appendix sections and index are a little different. The topics covered in the sets of appendix sections are not the same. Should I create two different pdfs with different appendix sections or create a single pdf with both sets? 2. One document is missing the title page and table of contents. Should the pdf just be what I have or should I create those pages for the pdf? Thanks, alan