You can do that. But you will need to remove it before your return will get accepted. You can also include it and file by mail but I would not recommend that.
You can sign into your IRS and print out your records that should show that it is paid (according to who you spoke to at the IRS). Here is the link to view your tax records. You can print out your account balance and keep it in case they ever attempt to bring it up again. But if they show it paid, they will refund you the money even if you do include it.
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