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What’s the recommended way to update an application to reflect recent grades? If, for example, Judge A only accepted paper applications, is it alright to email his/her JA or CDC with the updated transcript? Or is mailing the update the best/only way? Would appreciate feedback from current/past clerks or others with experience. Thanks!

Why don't you just call chambers and ask? I'm sure the judge's JA or clerk would be happy to tell you their preference.