I'd prefer that you didn't. I purposely left it unprocessed by Calibre because when you put it through Calibre, any paragraph that begins with an italicized word or one in bold print, will have an indentation that will be different from ordinary paragraphs. If the chapter dots are more important to you than how it looks, by all means run it through Calibre for your own use. I do that myself with some sci-fi books which I know I'm going to re-read, but which I also know will contain battle scenes I'd just as soon skip.
I'm assuming that when you say it now recognizes chapter breaks, you are talking about the chapter dots that appear in the reading progess bar. Prospective readers should know that the beginning of each chapter does begin on its own page and is reachable by a linked toc.
Thanks for the compliment, by the way. It took a while to do.