There is no need for concern. Below are the answers to your questions.
Do I ask to shred the printed 2020 forms? No. The IRS will discard them once they see a 2020 return has been filed and accepted.
Do I ask why the 2019 information doesn't match what was sent? Or even if the forms were ever received?
According to you, the transcript indicates no return was filed. You should send another copy of your 2019 tax return to the IRS with any income documents including W-2s. Be sure to sign the return before mailing. It's not clear why your income was a negative amount.
Do I mention the 2019 extension? The extension is not relevant at this point in time. The extension period is ended, therefore the use is not helpful in any way.
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