Pretty cool actually. In a way they still made these locations canon, just a lot further in the future.

This was from an early draft of the film. Instead of being banished to the Basalt Beach, the Mane Six were banished near a Hippogriff temple and spend the night in there. We can also see the Mane Six being upset because their quest of liberating Equestria from the Storm King has go up in smoke. While this doesn’t happened in the finished film, we do see some Hippogriff statues in the ruins of the Hippogriff kingdom. And they altered the Post Seaquestria scene by letting the Mane Six getting into a heated argument which leads to Twilight being captured by Tempest and Grubber and then take it back to the now slaughtered Equestria which is still ruled by the Storm King so he can use the Staff of Sacanas to drain the magic of the four alicorn princesses that the Storm King have overthrown earlier in the film and use the alicorn magic to create a huge storm to wipe out the entire cost of ponies and keeping ruling Equestria and the rest of the world while the new characters rallying the Mane Five and Spike to resume their chances of saving Equestria from the Storm King.