I received a cp2000 later from 2016 for the amount owed as 2,628. Will they withhold my current expected refund? Can I still file that 1099 from 2016?

[BMcCalpin · Accepted solution]

Do exactly what the CP2000 letter tells you to do - often, if you accept the additional tax caused by not reporting a 1099-R or a 1099-MISC, the letter will tell you that you do not need to amend your return (the IRS will do it for you). Read the letter carefully to see what the IRS wants you to do.

As for your current refund, the automated processing for e-filed return is handled differently than the letter audits like a CP2000, so while the IRS COULD take your refund to pay the tax bill from the CP2000, they probably won't, because they will send you your refund before the CP2000 process is finalized.

[Edited 3/11/2020 3:06 pm CDT - made year neutral]