Zero cost basis transactions are flagged by the TurboTax system because they're weird. "I sold a thing I didn't have to pay for" is a little weird. So it flags them. You have to go through each one and say the basis is ok. It's a little annoying. But it's sensible precaution.
Once you've gone through each transaction and said it was ok, though, then you should be fine. The same transaction won't pop up a second time.
@nirlay
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