Yes, you can file an amended Form 1040-X. It appears that the only item that requires new information is Part III where you can enter the reason why you are amending the return and you can also attach the amended Form 8606. Perhaps leaving the Form 8606 blank or perhaps adding an explanation in Part III that the original Form 8606 was prepared in error and that it should be discarded might suffice to correct the issue. Be sure to include in your explanation in Part III that the filing of the original Form 8606 in no way impacted the Form 1040 in that there was no IRA deduction taken, but it appears you already have this issue under control.
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