1st review your entries in TT to make sure that the refund you claimed is correct. if you can't find any errors then
respond to notice. write that you disagree with their proposed assessment . that your 1099-R from...... shows $xxx.xx in federal withholding that they haven't included. include a copy of the 1099 sign and date letter. send everything to address as indicated. send by method where you get proof of delivery.
if you find error's pay what's due
