There is no point doing just a redesign or redo of animations many hours into a game and there are two reasons, which are also scenarios, why:
#1 Redesigns of the characters and perhaps maps too; animations as well or just them, but these changes aren't applied for the previous content. This is jarring as you will see the old designs or animations transition into the new designs or animations, so you will not see one whole style which is not pleasing, as you want the old content to have the better content (this isn't always the case for a few things).
#2 The opposite happens where the old content gets the makeover too (it can just be characters, maps, or animations). However, this is actually an entire remake of the game though just the appearances of the characters, maps, animations or any combination of the three. So with this remake, you should add in new scenes and new content to make the old scenes better, and also include any content you couldn't before, since you have the time. This what Snats has done.
The original story hasn't been nuked, instead, he's adding onto it.