There are two things you can do. The first, and unfortunately, the best choice, is to amend the return as this will allow you to state the exact reason for the amendment and therefore the payment will get applied correctly to the "reason code" that it should get applied to. Some in past have just sent in (mailed CM/RRR) a copy of the incorrect return with a letter and a check (with SS# and short detail in memo field) and they have "squeaked by" unscathed, so to speak. However, given all the issues and troubles/confusion the IRS is having with 2019 and 2020 she's better off filing the amended return - in my professional opinion.
