I don’t take notes, annotate or even use a pen, pencil or highlighter when reading. I re-read interesting sections a few times (I am a very, very slow reader) and put the book away and mull over it. I take lots of breaks every few pages and this allows me time to absorb the essence of it.
Once it is absorbed, I feel it becomes part of your latticework of mental models and unconsciously affects the way you think. For eg. thinking fast and slow has changed so many aspects of my life from portfolio management (money management, risk management), trading psychology, general decisiveness to spirituality. When I sit back and think, I can point to the sections of the book the thoughts and ideas stem from but not during the process of it (happens subconsciously). I believe this is how each one of us is and there shouldn’t be a need to remember - it becomes part of you.