You can record a VAT-only invoice in QuickFile by making two lines, one for the net amount as 20% VAT and another at minus the net amount with no VAT, e.g.
- Motor expenses - repair costs following accident: £2,440 NET, 20% VAT = £488
- Motor expenses - Less: net paid by insurance: -£2,440 NET, no VAT
This gives you a purchase in QuickFile for £0 net plus £488 VAT.
When it comes to the VAT return I asked HMRC and they said I should include the net amount in box 7 even though I didn’t pay it myself, so I would make a manual adjustment to add £2440 to box 7 on the return (which doesn’t affect the VAT due so you don’t need to adjust for this anywhere else). I guess this makes sense as the main purpose of box 7 is as a cross check that you’re not trying to claim more than 20% of the box 7 value in box 3.