Could those sentences be used if each time one book was stolen from him?
Both 'a' and 'b' don't tell the exact number of books stolen from him. If the addressee knows that exact number, he / she will understand the speaker's intended meaning.
Is that one correct?
Could it be used if each time a different book was stolen from him.
It is correct, but funny, as it means that a certain book was stolen from him more than once. It doesn't convey your intended meaning above. I think you can better use your words above: He had three books. Each time, one book was stolen from him.