I use the highlighting and notes feature of my Kindle a lot. Even physical books I tend to write in the margins, dog ear pages, and underline passages. Especially for non-fiction, this process helps make reading a more participatory activity for me, and helps me retain the material better.
After finishing a book, I used to transcribe the notes somewhere like Evernote for future reference, but I frequently found these entries getting overlong, and almost impossible to navigate later. The reason, I’ve found, is because not everything you highlight in the moment is as significant once you get some distance from it.
Now after I finish a book, I set it aside for at least a week before reviewing my notes. Often, many of the highlights which seemed so important as I was reading have lost their value with time. This waiting period helps bring the best ideas and concepts, and ensures notes stay relevant and digestible in the future.
I suppose you could wait longer for even greater effect, but then I’d worry about actually transcribing the notes at all. A week feels just right.