I believe they're only available on Reborn, but you must purchase the route-exclusive miracle(s) before beating the final boss on the clear file you're using. So as long as you cycle with Reborn for the next three cycles and purchase the miracles each time, you should be able to get the full miracle list.

The sub being private means I can't scrape through my comment history (I've definitely answered this question before), but that's what I recall.