I think the only way we've found to do this is to build the book on Runestone with the questions visible so that they get added to the Runestone database, and then immediately modify the source to make those questions not visible and rebuild on Runestone. We've discussed having a "manifest only" attribute or something, but as far as I'm aware, that hasn't happened.
For example, you could add a pretext section that contains the questions, build and deploy, then comment out that section, rebuild and redeploy. Or use a PreTeXt component for all the sections you want as non-visible exercises and then have two publication files.
Would that work?
Chrissy