TOSCHESTATION on the TFN forums pointed out that early on in the book, Rinzler digs up a snippet of plot notes by Lucas which appear to be "pre-Empire":

"The Emperor is the evil one - he kills Luke's father. Vader begs Luke to kill him - he does."

These notes would appear to come from the liminal stage between ANH and ESB, when Lucas was reconsidering both the backstory of Father Skywalker and the notion that Vader was a dyed-in-the-wool irredeemable villain. But the obvious solution--to combine the two ideas into Father Vader--hadn't quite gelled yet.