Yes, if you can speak to someone at the IRS to explain your situation, that may be helpful. However, if your attempts to reach someone at the IRS prove unsuccessful, then prepare your return that way it should be prepared notwithstanding the Certification form. You need to prepare an accurate return, and if you are eligible to claim the capital gain exclusion, then claim it so that your return is accurate. In the future, you may need to explain to the IRS the conflict between the Certification form and your return; however, it appears you have the documentation you need to show why the Certification is not accurate and why your tax return is accurate.
@Bruce05
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