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Would you go back and restart with the changes you have in mind, or finish the story first, inlcuding the changes you plan for it, then go back and make needed changes during the editing part?
I would make minor changes in the existing draft. Often a few words will complete shift the meaning.
Anything major, I would finish the first draft and fix in draft 2. Alternatively, I would stop draft 1 at that point, save it as a new draft, and begin draft 2. It really depends on where I am in the story and how much has to change.
I would save the file with a new name, then redo the first part and then decide whether this is the way to go. If yes, I would continue writing the "new" plot.