Once a transaction is deleted from the system (ie a line item on an invoice or an entire invoice, or a sales receipt etc.) then it is gone forever, as if it never existed.  If this deleted transaction was previously filed in a VAT return, you will not be automatically credited back in the forthcoming VAT return.  If you would like to be credited back in the next return there are two options.

1. You could manually create a credit note for the transaction you deleted - if the invoice was for £100, you would create a new invoice for -£100.  
2. You could also create a journal entry (if you are running Cash Accounting, this is the option for you).  However, please note: only journals posted to Input VAT or Output VAT will be picked up in a VAT return.  Enable your journal via Settings -> Advanced Settings.

Viewing Deleted Transactions – need help remembering the data?

While you cannot recover deleted data, you can review and reference it with an Audit Trail Report (Tools & Reports).  Select a date range that includes when your deleted transactions were created or edited, tick the “include deleted items” box and tick the box beside the proper transaction.  When you run the report all deleted transactions will show in red.

What modifying transactions will do to your VAT return

If you modify a transaction that has already been filed then it will show again on your latest VAT return.