The notebook doesn't show up until Indy is in the WotS (and only in that scene). The theory goes that Marion either had separate living quarters from the bar, or the area of the bar that she lived was not yet engulfed in flames when they rushed in to grab a few things. Also, why would Indy have the Ark notebook. If the Ark was Abner's passion there would be no way he would give it up. He would probably keep it with the headpiece.