controller wrote:Several questions arise:
1) Are we liable to pay the VAT?
For those supplies (if any) which are outside of the 4 year limit for reclaiming your VAT - then it depends on your contractual terms and to some extent your relationship with the supplier as to whether the cost of the VAT is borne by them or you (or shared).
For those which you will be charged UK VAT, normal commercial procedure is for them to provide you with the respective invoice to evidence your claim for the VAT, you include this in your next VAT return, and once the VAT return is settled then you cash settle the VAT with your supplier.
controller wrote:2) If we were to pay the VAT, could it be reclaimed either
a) by the UK branch as a voluntary declaration
If releveant, can we use the hmrc's refusal to believe that the goods were removed from the UK as "proof" that the goods remained in the UK (even though they weren't!) and that the VAT can be reclaimed
It can be recovered, subject to the 4 year time limits, providing you have the VAT invoice. If there is any reason to suspect the supplier is not being truthful about the HMRC assessment then you should get a copy of their assessment/correspondance from HMRC - the supplier should be willing to provide if they want their VAT.
controller wrote:OR
b) by the EU branch under the electronic cross-border refund system?
if b), does the time limit for cross-border refunds of "no later than six months after the end of the ‘prescribed year’ in which you incurred the VAT" relate to the date the invoice is raised (Jan 2012) or the tax point date (2008)
No if you are VAT registered already in the UK, then you cannot submit a claim under the 8th Dir reclaim system.
My final advice would be to check what exactly the issue is with HMRC, is it that the goods weren't removed in good time or that the evidence wasn't sufficient? Are the goods a MTIC fraud type goods (computer chips/phone sim cards/mobile phones)? Usually a BOL would suffice...