My situation is exactly the same as yours, including filing my 2019 return in July 2020 and paying what I owed. This was the first paper return (and last) that I've filed in over 20 years. The website confirms that my payment was received, but there is no record of my return in the Transcript. Fortunately I was able to talk with a IRS rep on two occasions in the last month. Hint: I was successful by calling at the end of the week and near the end of the 5:00 pm business hours. They confirmed that they are behind with the processing. The IRS separates the returns from the payments immediately, cashing the checks, but the paper returns are put in the large backlogged pile for processing. The rep entered notes in my file stating that the payment was received on time and told me that it may take up to nine (9) more weeks for the return to be processed. She stated that I should not file my 2020 return until the 2019 return is processed, which means that I cannot claim the second stimulus payment, nor get my expected refund, until then. She requested that I check online on a weekly basis until it shows up in the transcript and that the IRS will not process your 2020 return without a record that your 2019 being processed. As of today, still no change. Good Luck To All Of You!!
