I'd say it's the same kind of subliminal consciousness that you would have of the tone of a conversation you're in. I feel the tone of my novel as I write it. There is maybe an early period where I'm trying out different tones, and then one clicks in and feels right, and maintaining it is a matter of keeping in touch with that feeling, or getting back in touch with it if I've been away a little too long. Best way to get back in touch with it tends to be reading what I previously wrote.
The one thing I've done more consciously is to try to put in more humor, b/c I'm not great at humor. But that's a matter of comic relief in a dark story; I don't know if you--or at least I--could work consciously to impose a particular overall tone and have that work.
I've never made such major changes that they'd require, or cause, a change in tone, so I can't speak to that last part.