A nice call to action. I look forward to seeing the results.

I’m currently writing my second book. It’s about how Charles Darwin looked at the world. I only discovered Zettelkasten and Obsidian when I was already a considerable way into the book, but, after using them for a while, so sold was I on their potential that I ended up taking several months off writing to build a retroactive vault for the stuff I’d already covered—as well as the stuff I was yet to cover. I’ve documented some of how I did this on my blog (though not in anything like the level of detail you’re looking for). Here’s a link to some pertinent posts (but do read/subscribe to my other stuff, obviously—we all need more readers!): http://richardcarter.com/tag/zettelkasten/?orderby=date&order=asc

As you’ll see from a couple of my more recent posts linked to above, using a Zettelkasten(ish) system has helped immensely in putting together a few of my more recent, rather complex chapters. It has allowed me to see the wood for the trees.

In terms of your call for examples, it’s difficult to break a complex process such as researching and writing a book into a single, linear workflow. It involves keeping lots of plates spinning at the same time. While working on my Darwin book, I’m also making notes for other potential books (on different topics), as well as notes about other stuff that also happens to interest me—some of which have resulted in longer-form blog posts (e.g. http://richardcarter.com/sidelines/nature-writings-ill-defined-thriving-ecosystem/).

(Off the top of my head…) A few of the key lessons I’ve learnt:

have a note-making system in place before you start your research. Putting one in place retroactively is a major headache!
don’t get too hung up on what constitutes an ‘atomic’ note; I write notes on single ‘topics’. If they start to get too long, I try to split them. Many of my notes would now probably count as ‘atomic’, but by no means all of them. What matters is that they’re useful to me.
once you’ve amassed enough notes around a particular major topic, you find linking between them enables you to shorten many of the notes;
once you reach the stage where certain notes have evolved from longform notes into (mostly) an organised set of links to other notes (which I refuse to call a MOC), you’ve probably got good material for a chapter. In fact, you’ve got the beginning of a chapter outline;
have a note for each chapter you plan to write, so you can begin to link ideas together. (c.f. https://notes.andymatuschak.org/Create_speculative_outlines_while_you_write)
construct your chapter outline inside your chapter note using indented bullet-points. Each major bullet point (and many of the minor ones) should link to or reference an existing note. If you find they don’t, you’ve probably identified an area requiring more research (or an area that doesn’t belong in the chapter).
don’t try to write your actual chapters in your note-making app. Keep your notes and what you construct out of them separate. (I often break this rule when drafting blog posts, but I always delete the draft from my vault once I publish the post.)

I should probably write a blog post or two about this some time!