How to deal with a VAT exception created by receipt of a late invoice

Hello KimW2023, 

Welcome to the Community page, 

Here is some information regarding expectations. So you understand that exceptions are created when you make changes to transactions that have already been filed in a VAT return within QuickBooks Online So if ever that, you have made changes in the past, with entries that have been submitted already in QBO. That would be a genuine exception and is expected to happen. So it would be a case of it is meant to be there so dont need to do anything with it.