I recommend that you file an extension while you work to resolve this situation. Determine whether you will receive a refund or owe, based on what you believer are the correct amounts. If it results in a balance due, pay the balance due with your extension. Do this for federal and state, if applicable. Hopefully you will have the issue resolved well before the October 15 extended deadline.
If it is getting close to that deadline without resolution then I suggest you contact the Taxpayer Advocate Service. They are an an independent organization within the IRS. They can help if you have tax problems that you can’t resolve on your own.
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