The simplest solution is as follows:
- Record the accidental payment as a Cheque payment to HMRC, but make it as a payment to Accounts Payable for HMRC as well. That way it will simply appear as an available credit.
- Process VAT in the normal way, and when I come to pay simply apply the duplicate payment as a credit.
- Presto! The final amount owed matches the amount collected by HMRC.
Don't know why I didn't think of that in the first place.
