The way that amended returns work, they report the net difference from the original return. That is, if you got a $3,000 refund on your original return, and the amendment process did not change your tax due or refund, then the refund for the amendment should be zero.
Note that you will receive the $3,000 anyway, because the amendment process is independent of the e-filing process.
And if when you added the 1099-SA, you said that all distributions were for qualified medical expenses, then your tax due or refund indeed should not have changed. All you have done is corrected the paperwork (which may have saved you a letter from the IRS, because the IRS already has a copy of the 1099-SA and would have wondered why you didn't report its numbers on the 8889).
So don't worry, you'll get your original refund.
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