Can you tell us a bit about where the tax withholding came from that resulted in your refund? Was there "voluntary federal withholding" on your Social Security 1099? (1099-SA)
It sounds like the IRS can't match up the withholdings (or estimated payments) with their records.
If you see "voluntary federal withholding" on the 1099-SSA, send copies of those with your reply to the IRS. If you don't see withholding there, send the documents in where you do. The IRS should be able to then reconcile the data to process your refund.
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