Bone Edits Without Messing Up The Model?

[KingJigglypuff]

I have been wondering how to do this for a while.

I want to edit a model's bone translations without having to go though each of the animations and changing them. But whenever I do it by going to frame 0, the model screws up.
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Like what Beyond did with his Scott Pilgrim vertex. How did he edit his model's bones without screwing them up?