I could see a fairly simple reason why the emperor would change projects after the Chaos gods stole the primarchs away; He decided to stop putting all his eggs in one basket.

As for the primarch notes stuff being unreproducible; A) I think some of them were lost somewhere down the line, or controlling the Canis Helix would not have been the monumental feat of research it was. and B) I don't think it's unreasonable to suggest that the Emperor's notes involved concepts that the Imperium lost somewhere during the next few millenia after putting him on life support.