Because doing the opposite replacement is not the same as undoing a replacement.
What happens if you already have valid uses of the replaced-by word?
That will very likely be the case -- and your proposed "go through it one by one" is slow. It would probably be faster to redo all the correct spelling fixes (they are usually less ambiguous and possibly less numerous too).
I'd rather undo all correct spelling changes, to get into a known good (or at least better than when I first started out) state, then redo all the spelling fixes. It really does seem to me to be the safest route.
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