Assuming you have everything in a single audio event on the timeline, you could convert the event to an audio part and then make cuts in that. For example, let’s say you have a spoken introduction, but there’s too much “dead air” between the intro and the start of chapter one; well, make a cut after the intro, another one just before ch. 1, then select and delete the audio part containing the dead air. That will leave you with two audio parts on the timeline, so you can then move the intro to the right until it butts against ch.1, leaving the rest of the work unaffected and still at the same absolute position on the timeline, so your subsequent notes will sync.
If I’ve understood correctly that would enable you to work from beginning to end, with the piece effectively getting shorter with each cut, but in a way in which the beginning of the piece starts later.
There would be other ways involving time offsets in the project, but that would involve messing with time calculations and would in my opinion be more susceptible to human error.
You should also investigate markers and the marker track, because that would allow you to drop markers as you listen to the work, the position of which could be fine-tuned later, and you could do a global split at each marker point, remove any unwanted sections and the best thing is the markers can be named and might be able to take the place of hand-written notes for you.