I'm currently rewatching A Certain Magical Index (including II) and A Certain Scientific Railgun (including S) in order by anime release date. Thus I've rewatched Miracle after II but before S. I remember S included a retelling of the strongest vs weakest plot from the original Index season, so this order doesn't in general match in-universe chronology. My attempt to place when Miracle occurs depends on the following facts:
- Uiharu is surprised to learn of a wheelchair-using Kuroko's early discharge from hospital, suggesting this predates her wheeling Kuroko during the Daihaseisai. In particular, Miracle would seem to slot between the Tree Diagram Remnant and Daihasei Festival arcs. (Because I haven't read the manga and don't remember S well, I'm familiar only with the Index arc for this festival.)
- When Index asks Touma what Endymion is, he mentions it's been visible before, including when she holds a grocery bag while standing next to him. This flashback is to footage from the end of the first II opening. This doesn't contradict the above placement of Miracle, although it does require said footage to occur early in (or before) II.
But there is an important subtlety:
The movie retcons several scenes from the Toaru Majutsu no Index anime to somehow fit the obvious elevator in the timeline. Toaru Kagaku no Railgun S would later insert the elevator into scenes where they were supposed to appear as shown in the movie.
In particular, the aforementioned flashbacks are doctored; for example, the II opening doesn't include Endymion.
My reading of all this is that Miracle occurs when I've suggested, but results in some retcons of certain scenes as appropriate. Am I right, or is the retconning more radical than that? If so, the timing of Uiharu learning of Kuroko's discharge could shift.