How to account for deposits paid up front for jobs ?

Client takes a 20% deposit for a job up front to secure the date and pay for materials. He invoices the amount paid for the deposit including VAT, so that it is reported on his VAT Return, and allocated to a liability account. When the full invoice is raised, he puts the deposit paid amount with no VAT, and a minus line item so that the balance due is correct. But this puts the liability account out of kilter because the payment includes the VAT, yet the amount billed excludes the VAT.  How do you resolve this ?