I would have thought that the usual procedure would be for the supplier to send you a credit. The only reason I can think of for you to invoice is if it is a contra charge for example they did something wrong that has cost your company money or you have actually supplied something to them.
In the latter case you would raise an invoice for the total value that you are due to receive and if your company is VAT registered work the VAT out backwards. Eg You are owed £100 so divide 100 by 120 times 100 to get the net figure (£83.33) then add the VAT on (£16.67) and the gross figure is £100 (assuming its a 20% rated service/goods)
It does depend on whether the rebate is a retrospective reduction in the price of the goods or services. The VAT liability will follow that of the original goods or services.
Or, it might be a bonus, which is generally outside the scope of VAT.
Check the paperwork, or ask for some!
