There is no way to file your return electronically after filing the non-filer submission, because that submission created a tax return entry for you, with all 0s on it and cannot be canceled. For security purposes, only one electronic submission per tax year per taxpayer is allowed.
You will need to print your return, and file by mail.
You should attach an explanation to your return indicating that this is a correction of a 0 return previously filed, or attach a blank copy of Form 1040X (signed) to the front of the return or make some other indication to let the IRS know that the return is intended to replace the original filing so that it is not rejected.
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