Yes, you can change the amount in box 12 that you enter into TurboTax and that will not change anything. That action simply eliminates the notification. The IRS has already received the W2 that you have a copy of. If the box 12 amount actually shows an over contribution through that one employer, then the taxable amount is likely in your wages (box 1) already.
Here is a link with more information on the topic.
You will likely get a form 1099R for 2024 that shows the excess contribution and earnings was distributed to you. Assuming the distribution is/was done before 15 Apr (which if the employer noted on your W2 already, that indicates it was done) you will avoid any early withdrawal penalty, however taxes will be due on any earnings on that excess contribution. This will be handled when you enter the 1099R information for your 2024 tax return.
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