How does Magical Citadel of Endymion work?
For most monster’s effects, you can only substitute spell counters from Magical Citadel of Endymion once per turn, because it says so. Arcanite Magician doesn’t need to substitute spell counters for it’s effect, since it can remove them from anywhere on the field, so you can remove as many counters from Magical Citadel of Endymion for Arcanite’s effect as you want per turn.