Quite a peculiar situation I must say. what did you end up doing in the end?
A great way to help prevent this in the future is by using a reliable software that will help take care of your VAT for you especially with Amazon/eBay and cross border selling. This is incredibly useful as I have learnt from my own experiences the types of complexities that can take place. I know of a software called Cross Border VAT who really helped me get all my VAT obligations correct as I sell to other EU countries