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The IRS probably only sends the letters to the first primary person listed on the Joint return.  I wouldn't worry about that.  There must be more they are questioning if they got your original return and sent you the refund.  You have to call the IRS and talk to them and find out what's going on. 

If you efiled there should be an Electronic Postmark page saying when you filed and when the IRS accepted it. Probably near the end.   Here's mine for 2024.