To delete a VAT return, go to Tools & Reports -> VAT Management reports -> Click on the submitted VAT return -> Delete (button in the bottom right hand corner).
Status - Pending/Complete:
When the VAT Return status shows as Pending, we would advise you not to delete it as it has been submitted to HMRC. If you delete it, it would be removed from your Tally account, but HMRC will still receive the return. Also, you will not receive any email from HMRC informing you about the VAT submission status. And so, we advise you to wait for a reply from HMRC before you delete the return or contact HMRC for best advice. The other status that would be more suitable for deletion is Error or Cancelled.
Consequences to deleting a return:
Once you have deleted the VAT return the journal that was created with it is also deleted automatically. If you delete a completed VAT return which has been submitted to HMRC, all the transactions that were in that period will be marked as not submitted or filed. As a result, they will end up in your latest VAT return which will be in most cases undesirable because you may have already paid or reclaimed that portion of VAT in the past for these transactions.