You're confusing two different things. 1 the court determined that apple subverted the original injunction, and ordered that it comply immediately (specifically calling out all the ways apple was getting around the injunction previously). 2 the court said that to issue a fine so that apple loses whatever money it gained by non-compliance would be considered a criminal matter (unless it becomes clear that there's no other way to force apple to comply with 1 above) even though it may be appropriate, and as such it is beyond the scope of what the court could order in its own, and the court refers the matter for criminal prosecution.

So this change is just apple complying with 1.