So you received a letter from the IRS telling you they found an issue with your return and they are working to correct it? If so, this means they are likely going to make changes to your return. Until you receive another letter with more instructions do not do anything. The instructions may be that they are making the changes and if you disagree with their findings then you can send in an amended form or if you agree with their findings to do nothing.
Since you already submitted your return, and it has been accepted by the IRS the only way to make changes is to Amend Your Return . You cannot simply refile a return, instead you have to sent the IRS a 1040X to let them know that you made a mistake. If you do end up needing to file an amended return, you will need to remove the changes you made to your return since you filed so you are starting with all the errors on your return. As you make changes with the 1040x, you will see the difference in refund and income amounts. But, again, do not file anything else until you get the next letter from the IRS.
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