Any advantage to proactively refiling previous-year paper tax return that the IRS misplaced, and that I have a paid balance on?

Question

I filed for the first time on paper in June 2020 for tax year 2019, and I have the certified mail receipt. I owed a balance, and the IRS deposited the check that I enclosed, but I didn't receive either of the 2020 stimulus payments, which I was eligible for, nor did I receive any correspondence from the IRS.
I wanted to see my 2019 record of account to try to figure out whether there was some reason I wasn't eligible for the stimulus payments (and I'd keep the transcript just for my records). Neither the Get My Transcript nor the Request Transcript irs.gov services would let me request the transcript because my details couldn't be verified.
I called the IRS, and the representative researched my account, finding that indeed they had credited my account for the payment, but that they had no record of my return. He advised me to resend the same 2019 return with a statement explaining that this was a refile. However, if I did refile, I'd be contravening the IRS Covid operations webpage, which states

Other than responding to any requests for information promptly, there’s no action you can take. We’re working hard to get through the backlog. Please don’t file a second tax return or contact the IRS about the status of your return.

I'm not in a rush to get my transcript; my return could be in one of their trailers of Covid-delayed paper returns and might still eventually be processed.
Should I obey the customer service representative and refile my previous-year return, since the IRS seem to have lost my original paper return, or should I obey the website and hold off refiling until the IRS provides a written instruction to file, since the IRS might still be working through the backlog of returns?

Ben Miller - Remember Monica · Accepted Answer

If it was me, I would probably wait to file another 2019 return.
In early December 2020, the IRS commissioner announced that they were still sitting on 1 million unprocessed 2019 paper tax returns, and 3 million pieces of unopened correspondence.  Most likely, your tax return is in that stack.
As you noted, the IRS notes on a webpage about COVID-related delays that they are still working through 2019 forms and they are asking people not to resend returns until asked.
Stimulus checks in 2021 have not been finalized yet, so it is impossible to say how they will work.  They might be based on your 2019 tax return, and if so, you might not get them until your tax return is processed.  But sending in your return again does not guarantee that the duplicate will be processed any faster than the original.  And if you miss out on stimulus checks now, most likely it will be made right next year in the form of a tax credit, similar to the relationship between the 2020 stimulus checks and the Recovery Rebate Tax Credit.
If you do choose to send a duplicate return, make sure that you include a letter stating that it is a duplicate return of one already sent, and why you are sending it, so that they know that you aren't simply sending it in late if they happen to open the second one before the first one.

RonJohn · Answer

Absolutely refile the return:

accounting software needs to know where money came from.
they know you needed to file a return, so at some point will come looking for it.

And do it electronically, since this is the 21st century.

Any advantage to proactively refiling previous-year paper tax return that the IRS misplaced, and that I have a paid balance on?

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