Commuting miles, for a home-office-based self-employed person, are the first trip away from home and the last trip back and these are not deductible as business miles. So, you should have been deducting commuting miles for your business trips that started from your home office. The box for Commuting Miles in TurboTax is basically a reminder for this rule and it is not actually reported anywhere. Now that you are actually "commuting", you do not need to report or track them, just continue not claiming them as business miles.
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