Let's have a look.
"After the characters defeat the first prophet, run 'Dire Tidings' ...". OK, so in your case, that was Aerisi. "Dire Tidings" says nothing about it being the same cult that was just defeated. It could have been any of the cults that did it.
"After the characters force a second cult to abandon its shrine, run the 'Reckless Hate' encounter ...". In your case, this is the water cult. "Reckless Hate" *does* specify that the "offended cult strikes back", so in this case, you would use water cultists to carry out this retaliation. Perhaps one of the other cult leaders is directing them, if Gar is dead or has retreated to the water node.
"After the characters force the third cult to abandon its shrine, run the 'Race to Destruction' encounter." In this case, it's the earth cult. However, "Race to Destruction" indicates that the "remaining cult" sends a force. So here is where you'd use the fire cult.
After your PCs have wiped out the fourth temple, then presumably the four prophets are all either dead or down in their respective nodes (or in the fane). The PCs have dealt enough of a blow to the cults' machinations that they are too disorganized - and their numbers too depleted - to mount any kind of retaliation now.
However, you now have the option of running the "Haayon the Punisher" and "Counsel of Despair" encounters, as well as the "Wrath of the Elements" events.