It shouldn't be an issue - I've only ever stored the challenge/response in the ldap directory (aux class for the Pwm schema), but in that case it stores both the question AND the response per user on the user object. I suspect it'd be the same if you were storing it in the database. I got rid of most of the standard questions and put new ones in years ago.
If you do want to invalidate old questions (because they're too "known"), I believe you'd have to create the new questions, remove the old, and clear the user responses and force them to set new ones.