You didn't tell us the citizenship of the father, but it seems fairly obvious that he's not a U.S. citizen.  I would file a paper 1040, mark it "SUPERSEDING RETURN" at the top margin, and document that you mailed it by July 15.  

These instructions from IRS probably should have been rewritten after the law was changed to require an SSN for the CTC, but the part about getting the SSN before the due date of the return should still be correct (someone will let us know if it isn't).  

Note: If you don’t have a TIN by the due date of your return (including extensions), you may not claim the CTC/ACTC on either your original or an amended return. However, if you apply for an ITIN on or before the due date of your return (including extensions) and the IRS issues you an ITIN as a result of the application, the IRS will consider your ITIN as issued on or before the due date of your return. Also, you may not claim the credit on either your original or an amended return for a child who doesn't have an SSN by the due date of your return (including extensions), even if that child later gets an SSN.

https://www.irs.gov/faqs/childcare-credit-other-credits/child-tax-credit/child-tax-credit-4