Its been 13 months since I mailed my 2019 Tax Return with payment. The payment cleared my bank within 2 days. The IRS web site shows no 2019 Transcript but does show payment. When I dive in deeper it shows a status of non filer. The IRS told me to send a duplicate return which I did but I have determined that was a mistake. I received a letter from the IRS asking for my 2019 tax return and I responded with a tracking letter stating I had already sent in two and I would not send in a third. They have never responding to any correspondence. The IRS phone numbers are no help because depending on what day of the week it is and who you get you get different answers. I had to e-file 2020 tax return with my prior year AGI as $0.00 to get it to be accepted. I am tired of hearing the excuse of COVID.
If you attached the payment to the return, that would have eliminated the return being filed. If the check was separate, the return should have been filed. You said they asked for another return. It is common to ask for parts. Until they get all the parts, it won't be considered filed. If the IRS files a return for you, it will not have any itemizing, no cost basis, anything that would add value to your return so that you could potentially owe more.