So you got a letter from the IRS, right?
Did it tell you to amend your return? Often, with arithmetic errors, the IRS will just send you a a letter explaining the changed calculation and asking for the amount due if you accept the change. In this case, you don't do an amended return.
However, I can see that in this case, you might not have the money at hand, because the IRS (presumably) has your original refund.
I would reply to their letter (you have the address of the office and maybe even the name of an agent, right?) and say that you accept the change in calculation but that you cannot pay at the moment because you do not know where the $3,000 refund went. And can they help you find it?
It's possible that your situation caused your return to be placed in a hold queue, which they should be able to release, once you tell them that you accept their change.
Give them a chance to help you out.
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