VAT refund

Hello, I have a question about VAT refunds. British limited company recently received information from Amazon that they unmet UK business establishment requirements and Amazon will collect and pay VAT to HMRC from the beginning of the company's sales on Amazon. Until now, the company has paid the VAT on the sale itself. In such a situation, when Amazon pays the VAT on all sales retrospectively, will the company automatically receive a refund of the VAT already paid or should a correction of the VAT return be submitted? If a correction to the vat return has to be submitted, can it be submitted earlier before Amazon deducts this vat or does amazon have to deduct it first and a correction has to be submitted later? Thank you in advance!

Hi Emma12,
If a business believes that they have overpaid VAT on their VAT returns then they must submit an error correction to HMRC through the guidance here:- 
How to correct VAT errors and make adjustments or claims (VAT Notice 700/45).
You should submit this correction as quickly as possible after discovering the error.
HMRC will be unable to process any refund of overpaid VAT without the VAT returns being corrected.
If you are worried about being able to meet VAT payments owed to HMRC, or you anticipate that payments coming due will cause  problems, we would encourage you to set up a self-service time to pay arrangement while the situation is resolved.
This can be done online and there is more information at If you cannot pay your tax bill on time
If you cannot set up a time to pay arrangement online, you can call HMRC’s debt management team on 0300 200 3887. 
Thank you.