Was this notice from the IRS relatively recent?
If so, I would reply to the letter (they want a reply anyway (if for nothing that you accept their correction), and tell them about this other issue and ask them if they would make this other correct as well (and that you accept their initial correction).
The office(s) that generate these letters have the power to amend your return (as you can see), so give them to chance to (1) save you and the IRS some paperwork, or (2) tell you how they would like you to handle it (like amending).
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