How can just processing a refund, without it being applied to a valid VAT invoice or credit note be correct? There is no 'source document' if you just pay a refund, what do you have to back-up the recovery of the VAT on the money repaid to the customer? Your original VAT invoice has not been amended, so you must have a VAT credit note to reduce the amount owed to you by the customer. If the customer has nothing to offset that against, then you have to be able to pay the credit note.
I think Kevin's suggestion is actually the ONLY workaround to this that can safely be used, the ClearBooks process is flawed.
I would be happy to be proved wrong however, please!