Level 14
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No, you don't file a 1040-X to close a CP-2000 case.

It is unclear what happened here, but maybe IRS proposed $X in tax, taxpayers answered that they only owe $(X--Y), and IRS agreed to the new amount, let's call it $Z.  

If that is the case, then IRS should send a recomputed CP-2000 that client (both, if joint) can sign as the agreement to $Z.  They can send a check with it also, or wait for a bill.

Don't agree to the Section 6662 penalty unless you see the supervisory approval.