Did you report the sale? When I sold my primary residence in 2018, it ended up on Schedule D and Form 8949, and there were no questions asked. The IRS does have a tendency to assume zero basis when there's a capital sale reported to them that doesn't appear in the tax return; which makes for scary bills, but can usually be resolved by reporting the sale and your basis on the appropriate form. (although I see from further replies that you are now having to deal with this in Tax Court, so that sounds like a terrible time, and I'm sorry for your tedium)