Games Workshop have used their What’s new blog to post a clarification on their recently released 40K Witch Hunters and Daemonhunters codexs. Emphasis below was added by TGN.
From their website:
We recently made the Witch Hunters and Daemonhunters codexes available to download as PDFs. Since then, we’ve received a spate of emails asking questions about the difference between the PDFs and the original, printed copies. Rather than reply to you all individually, I thought I’d try to answer your questions here. Firstly, the rules for allied Space Marines and Inducted Imperial Guard were originally written to reference books that have since gone out of print, so we streamlined the rules required to allow players to collect an army of Daemonhunters or Witch Hunters. The Daemonhunters army list uses the Standard Force Organisation chart, which you’ll find on page 87 of the Warhammer 40,000 rulebook.
The other point that seems to be causing the most confusion is whether or not the PDF versions supersede the printed versions. They don’t: you should feel free to continue to use whatever resources you have available to play your games with; the PDF does not overrule or invalidate the printed Codex book. Yes, this may mean that you and your opponent are using what are essentially different army lists for the same army but not every Inquisition force will comprise of the same elements (highly specialised and secretive forces that they are). And if you’d rather use the same one as your opponent, why not simply decide which version you collectively want to use and share the rules between one another? As for tournaments and gaming events, it’s entirely up to the organisers to decide which version to use; it is after all their event.