There isn't a way to clear auto-scoring from a questionnaire, since once a score has been entered (even manually) it can't be deleted, simply replaced. However, you can tell that a question has been auto-scored because the Comment field will mention so, as in the screenshot below:
Therefore the best method right now to "clear" auto-scored questions is to review each response like you normally would, and then delete the auto-score comment once you've finished scoring the response manually.
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