There's not an indication on Form 1099-R that your distribution was a QCD. After you enter your 1099-R, TurboTax will ask you follow-up questions. You will select that your distribution was a Qualified Charitable Distribution.
The full amount of the distribution reported on your Form 1099-R will be on line 4a (IRA Distributions) of your Form 1040 or 1040-SR. The taxable amount reported on Line 4b will be the total distribution less the QCD amount and will have "QCD" entered next to it.
Refer to the TurboTax Help article What is a Qualified Charitable Distribution? for more information.
If you didn't answer the follow-up questions indicating that your distribution was a QCD, that may be why you received the CP2000 notice. You will need to follow the directions on your notice to let the IRS know that you had a QCD.
Refer to the TurboTax article I got a CP2000 notice from the IRS for more information.
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