Let me explain to you further about claiming back a VAT for a vehicle using the Flat Rate Scheme (FRS) in QuickBooks Online.
The FRS is already a discounted rate when you purchase a new vehicle. You can only claim the VAT amount if the capital of your van is above £2000.
Here's how to claim it:
Go to the Plus icon at the top.
Choose Expense under Vendor.
Complete the needed information.
Put a check-mark in the VAT Reclaimable box on the expense page.
Hit Save and close.
By putting a check-mark on the VAT reclaimable, the amount will post to box 4 of your VAT reclaimed on purchases on your return.
However, if the principal is below £2000, you're unable to claim it. For more details, check out this article: UK Flat Rate Scheme: How does it work?. Directly go to the bottom part.
I'm also adding here some links that you can check out about modifying items and submitting a return in QuickBooks Online for your reference: