Is the endeavor of a person who authored a book for the sake of Allah and published it for free, then wanted to add new information to it and issue it through a publishing house, considered a breach of his covenant with Allah, and what is the expiation for that?

What you have committed yourself to—making the book an endowment (waqf) for the sake of Allah, whether by spoken word or by publishing it online with the intention of waqf—is considered a binding waqf from which there is no turning back. An endowment becomes binding by declaration or by an action accompanied by the intention. What has been endowed cannot be reclaimed, for the example of one who takes back his charity is like a dog that vomits and then returns to its vomit. A waqf is a binding contract that cannot be rescinded or altered. The book is considered an endowment even if you retain the right to edit and add to it, and it is not a condition that it be removed from the possession of the endower. If you wish to re-print the book, you may do so without profiting from it; the publishing house takes its printing fees, and the book is sold at cost price. The best approach is to make the book available as an electronic copy for everyone online.