I had a number of clients receive notices in November 2020 saying they had not filed their 2019 returns (speedy IRS!) when all of them had valid extensions and all had accepted returns before October 15th, 2020. It sounds as if your letter is part of the same mess.  If I remember correctly, @sjrcpa  replied in early 2021 saying there had been 500,000 incorrect notices sent out about this.