Watch the scale and scope of what you're doing. If you read a book and make a hundred highlights and small notes, DO NOT attempt to turn all of these into permanent notes. You might fell like that is the thing to do, but resist it. A large portion are small things or potentially useful facts that you'll likely never use again or would easily remember, particularly once you've read a whole book.

Find the much smaller subset (5-10% or less of the overall total of notes and highlights as a ballpark rule of thumb) of the most interesting and potentially long term useful ones, and turn those into your permanent notes. Anything beyond this is sure to cause overwhelm. Also don't think that your permanent notes need to be spectacular, awesome, or even bordering on "perfect". They just need to be useful enough for you.

If you own the books or keep your brief notes and highlights written down and need them in the future, you'll still have those to search/find and do something with later as a backstop just in case.