You can only electronically file your original 1040 form once. Was your first attempt at electronically filing rejected? If so, then only your second return was submitted. Check your e-file status to confirm which return was filed and accepted.
Since you know your tax liability amount would be higher if you had included Form 8962, you can always reach out to the IRS directly for guidance on how to send in your Form 8962 and revised 1040 form since you have not yet received a 12C letter.
Understanding your Letter 12C
Contact your local IRS office
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