This seems to be par for the course for Pixar. I remember many of the deleted scenes from the Inside Out DVD were prefaced with explanation from Pixar that they were from a much earlier draft. They realized after working through the first draft that they now had a much better understanding of the characters, and then rewrote the narrative to match.
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This decision came fairly late in the process, as animators had been working on the film for almost a year with only 17 months until it needed to be completed.
Nobody comes into a digital movie with all of their tools already written and running at top speed, right? Isn't this typically a process where frames per hour is pretty low at first and ramps up as you go?
