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Yes. They won't take the fees out again. But they might take the 39.99 Pay with Refund fee if they didn't take it the first time.
If the IRS releases your refund after you've paid your TurboTax fees, we won't deduct your TurboTax fees twice. However, we still deduct the Refund Processing fee.
Here's the FAQ for that.....
If the IRS took too long to send your refund and you paid the fees out of pocket then see step 3 under What happens if the IRS reduces my refund......
https://ttlc.intuit.com/community/payments/help/what-if-my-federal-refund-isn-t-enough-to-cover-my-t...
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