Just had a client send me a scan of a refund cheque for VAT, to ask if it was correct. Turns out HMRC took the sales VAT from the bank, disregarding the input VAT, despite that the return was correct. Luckily this client had the funds to cover the £4k overpayment!!!
Client had £nil sales VAT and £4k purchases VAT so were due a VAT refund of £4k but HMRC were going to take £4k rather than pay them £4k.
Turns out was an issue with Taxcalc software, which I use to submit my VAT returns. The client had changed from annual accounting to quarterly VAT and because of this something didnt get picked up correctly in their software.