You wait for the letter. When you have a difference that large, that's a good indication that the IRS found a problem/error on your filed and accepted return, and they just fixed it for you. When that happens and it changes your refund, the IRS will send you a letter explaining what they changed, why they changed it, and what actions to take if you dispute the change. That letter will have a "respond by" deadline on it. So if you dispute the changes and don't respond by the date indicated in the letter, you lose and there is no recourse. Additionally, that letter will have a phone number that you can call if you have any questions.
Generally, it's about 3-4 weeks after your refund is issued, before you receive the letter. So all you can do is wait at this point.
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