This is a difficult idea to articulate, but I'm going to give it a shot. I'm in the process of revising a novel right now, and I'm in that part of the revision process where I sit back and try to figure out what exactly I need to change. It's a pretty holistic process: once I decide that a book needs to be revised, everything becomes up-for-grabs, and I'm willing to make the most drastic changes I can imagine.
But oftentimes I don't need to, because the novel itself is telling me what I need to change. Over and over again, I find that works-in-progress contains weak spots: placeholder characters or scenes or objects that I need to flesh out in order to complete the book. It's not that I purposefully left a blank in the book when I was drafting, it's just that a book, in order to be complete, needs to have a certain shape, and my subconscious, sensing this, put in something that'd make it so the book had more or less the right shape.
For instance, in the current draft, one of the characters has a boyfriend character who's sort of hanging out, not doing much. But meanwhile I needed to figure out something to create tension between this character and another main character, and I was like, oh wait, the boyfriend: he doesn't like the other main character. That's it, that's what he's doing.
Now the boyfriend has been in the book since the first draft (written literally years ago), and he's never really had much shape or pulled any sort of weight, but I knew he needed to be there, in order to represent whatever it was that kept this character tied to the real world (this is a fantasy novel).
I've also had this other amorphous character--a villain who was defeated long before the start of the book--called the Goddess's Daughter, and in my recent revision thoughts, I realized that I can use her to provide a backstory for another character. The point is, she always needed to be there, but I didn't always have exactly the right use for her.
Which is not to say that you don't take things out. It's just that I've noticed that, overall, the process of revision ought to make the book less complicated and more elegant. Revision is where the book starts to feel like, oh wow, the author was planning this all along (even though he wasn't). It's also where I start to think, "What's this story really about? Where does the thematic weight lay? What is each character's arc?"
Oftentimes in early drafts, the book is propelled forward by pure longing, which is to say that what I've successfully created is a need in the heart of the character. But that need is itself an empty space, and in later drafts I need to flesh out the nature of the need: where did it come from and why is it still unfilled? (Of course this is all lies, since real life human beings are, in truth, rarely so uncomplicated that our needs can be clearly explicated, but still, fiction requires these lies).
This book is unique in that I didn't really know what my ending was going to be (except in broad strokes). Part of this was because I hate all that nerdy world-building stuff, especially the part where you have to explain the magic system. In my view, the magic system is that it works by magic. But that poses problems when you need to finally wrap things up. Because of this, I finally need to go back and think a little bit about how things work. It's just as intensely boring as I always thought it would be, and as a result I'm thinking about what ending I really want. Originally I'd intended a whiz-bang magical ending, where the hero conquers some external obstacle to defeat the bad guys, but I'm thinking that's not where my interest lies, and now I'm pondering ways to sap some of the drama from the third act.
Paradoxically, much of my progress as a writer has been about reducing tension, reducing excitement, and slowing down the pace. I know this doesn't sit well with some editors and some readers, but most of my favorite books take place at a more human scale (to put it bluntly, nobody gets shot in Pride and Prejudice), and I sort of can't tolerate the adventure story, since, to me, the entire narrative hinges on chance: the hero is the hero simply because an arrow doesn't hit them in the chest. If an arrow did hit them, they'd be dead and ergo not the hero. But we know, from real life, that no amount of confidence and skill makes you immune to arrows.
(As an aside, I'm listening to the audiobook of Ron Chernow's biography of Ulysses S. Grant, and what I love the most about it is the role that chance plays in Grant's life. In private life, he's a terrible businessperson, and in his personal nature he seems to be somewhat diffident and retiring. It's only the chance that puts him in the right place at the right time that allows him to shine as a general. This biography is rare in that it doesn't downplay its subject's virtues, but it also doesn't exaggerate them. Grant is, above all, a lucky man. It makes me see my own world differently. If the clerk at the tannery in a small town in Illinois could, in the right circumstances, become a successful general and, eventually, the president of the United States, then who's to say my plumber couldn't have been a great novelist or that my hairdresser might not've made an excellent Emperor. The world is a far stranger thing than we can imagine, and whether you call it chance or you call it fate, outside factors have a much bigger influence on our lives than anything we're able personally to do.)