For future reference, when you’ve updated your Libreoffice document so everything uses paragraph and character styles and there should be no direct formatting, and you think, ‘OK, now I’m going to use Clear Direct Formatting to remove any remaining formatting and I’ll fix it up if I missed any’…
Clear Direct Formatting doesn’t just clear formatting, it also removes all your page breaks between chapters. So then you have to go back and put them all in again.
Because that’s just such an obvious side-effect of selecting it.
It also seems to have changed some of the text into a different style, for good measure. What a pain.