It probably sounds backwards, and it’s certainly effort on your part, but you should file using the Form W-2 with the information provided, even though the withholding should not have been made.
Entering a W-2 with information that’s inconsistent with what the IRS has received could lead to even more problems -- such as the IRS contacting you because they don’t know why you entered the W-2 as you did.
Then, yes, send in the amended 1040X.
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