I agree, this does echo the good dinosaur. Cracking story beats and massively overhauling the film is quite common. In fact I attended a panel at D23 where the lot of animated directors basically said so. Domee Shi was on the panel and there was obviously a lot of comments that were about Elio without saying so. But unlike things like Frozen, Tangled or Zootopia, this represents a very late overhaul and a film delay. After significant publically released concept and footage. Which only really happened with Good Dinosaur.
Though the good dinosaur also replaced nearly its entire voice cast. That was quite something. This only shed America Ferrara due to scheduling conflicts.
The only time I can think of something having worked out, like this example, is Rogue One.