My client got a notice from IRS to pay more tax owed for missing a W2 for 2020. IRS notice did not request amend 2020 return.

Now I recalculated by add this missed W2 come up a much less tax liability, 

Was wondering if we should file an amend return?

Also another issue identified:

Combined the two W2's, total Roth 401k over contributed by $900 for 2020.

What is the solution to the over contribution Roth 401k for 2020?

401k Admin (Fidelity) told them it is passed the dateline to withdrew 2020 excess contribution>

my question, is it still ok to do early withdrew for the excess contribution?

Client concerns is that 1099 R will not indicate this is withdrew from 2020 excess contribution