Then you'll have to contact your accountant. You'll need to resubmit a manual Vat adjustment. Use the double entry system to make those amendments in Bullet. He/She might suggest otherwise though. So good to talk to them. It's a pain though. The government mainly wants the correct Vat paid. Not too concerned when.
Bullet won't know it's a duplicate and will have added the vat twice to the return. If you happy with it then do the following. Just click tax, the vat return in question and click 'unpaid'. (Remember the date of payment and back account) Make your edits to the bill and then click paid. That's it.