Hi,
If you were a NETP during that time, then it would have been the responsibility of the marketplace to have accounted for the VAT on the sale of the goods. If you have paid this over to HMRC then you would need to complete a VAT 652 and you will complete these for each period. You can see guidance here:
Tell HMRC about errors in your VAT Return
You would not need to request anything from Amazon but please detail on the VAT 652 the reason for the correction.
Thank you.