I would never delete my own archive of notes, because it contains a different kind of information: howtos for things I do infrequently, current state for personal projects I rotate in and out of over years, maintenance logs for my vehicles, identification details for every important account (account numbers, insurance expiry details etc).
When I'm doing something complex, I narrate what I'm doing in my notes. Most of these logs are write only. They can help as a kind of written rubber duck. And about 1 in 100 turn out to be extremely useful when I want to remember how I did something 10 years ago.
I use the same app (of my own design) with a different storage at work, and there I use it to remind myself what I did for performance reviews. Every edit is logged with a timestamp and I have a different tool which puts all the edits into chronological order.
For the author, their system served as a way of dealing with anxiety over self-improvement, it seems. But it turned into an anxiety of its own when the weight of unexplored ambition became manifest. It wasn't really a second brain IMO.