Now I wish Devonthink Pro had a feature like this. I've been using paper notebooks for years—this: https://jseliger.wordpress.com/2012/05/25/design-y-notebook-... discusses a recent example—and like you I find the reconciliation process difficult too. But at the same time, I find that I'm in a different "state" when I write on paper, and that's not a state I'm willing to give up without a good replacement.