The post-it gets stuck to cover the bits I don't want to photocopy, then I photocopy it, and then I remove it. As post-it-notes were developed to mark someone's place in a hymnal, I feel comfortable using them on my holy books, as long as I'm not leaving it on for years at a time.

That said, my mother's siddur that she uses to lead services from is all marked up with post-its that have, some of them, been there for years, and no damage yet. . .