I'd like to see Fate's answer to this first. I'm not sure there's enough information included in the question this time. A permanent miracle on a champion comes in a vast, many varieties. Everything from "I turn their skin vibrant orange" to "I endow them with natural claws and scales which add to their body score in combat." Then there are the example champions in the NGH where you have examples of actual spell caster heroes that have powers they can activate in combat.
In regards to champions and heroes, permanent miracles are very situation specific, and I was answering the original question from the concept of "I erect a wall of seawater and kelp at the edge of the harbor to keep out enemy ships."
Honestly, it all depends on when you spend belief, whether it creates conflicts or affects conflicts, and whether your followers are present to witness the miracle. It's kind of a judgment call for the GM (Fate). The bigger question is "Does it HELP your people?" If the answer is yes, then it counts during maintenance. I don't think how many times it helps your people comes into question though. In that regard, I don't know what to tell you.