I'd like to ensure that you'll be able to clear out the entries that are showing on your VAT tax exemption report in QuickBooks Online.
When deleting or changing some entries from your previously filed transactions, these will still show as VAT exemptions on your current VAT return.
To remove the transactions from the return, you can create a VAT adjustment. Please follow the steps found on this link on how to do this process: Adjust your VAT liability.
For more information on how VAT exceptions, reports, and submitting a return in QuickBooks Online, you may check out these resources below: