IRS Changed 2018 tax return

The IRS changed my 2018 tax return due to deceased spouses' trustee filing a different tax return as married, filing separately a month after I filed as married, filing jointly.   IRS then redid the taxes without including allowable tax deductions and ended up saying I owed them thousands of dollars, plus interest.  Can I still send an amended tax return that proves they need to repay the money they said I had to pay and the 2021 return $$ they confiscated?  Any suggestions or advice would be appreciated.