We have an urgent issue, our VAT reg no. has been rejected. We were told to contact the local tax authority, which we did (HMRC) they told us this number was perfectly valid. Our business registration number is also invalid (How can this be possible?!) We are now expected to make 50+ invoices manually for fba orders as amazon automated invoice no longer works due to the numbers being invalid. Not only that, our sales are massively impacted in a bad way too. the VAT number has been valid for 12+ years and now in the blink of an eye it has been rejected. Obviously a mistake, but cannot get past amazons poor automated responses and phone calls that say "we will get back to you" which is a complete lie and never happens.
I would guess it's because your business name on Amazon is slightly different to what shows on the VAT page (Ltd vs Limi).
Common sense can be hard to come by when it comes to these VAT checks.
I had a problem a couple of weeks ago, was all sorted via email and was suprisingly easy, vat-number-appeals at amazon.com
Hope this helps