Income received in 2020 but W2 was filed in 2019 and IRS proposed tax owe with penalty and interest for 2019

Hi, a finance institute issued us a NQDC distribution check in 1999 but we did not receive the check nor the W2. So we were not aware of the the income and did not include it in our tax return of 1999.  In 2020, another check was issued but no W2.  It was missed again when preparing for the tax return of 2020. Now IRS sent a letter asking tax owe for 2019 and penalty plus interest.  Should I file 1040X in this case? If yes, which year should I file? What is the chance that the IRS will waive the penalty and interest? Tried to call IRS [phone number removed] but could not get hold of any agent. Thanks!