VAT return submitted covering July August September, need to amend an invoice dated 24th September, won't let me as we are in Flat Rate scheme. How do i delete invoice?

Hello and welcome to the Community, mail51. Because of the way MTD works on the Flat Rate Scheme, you can't edit or delete transactions in a return that has already been filed.

If you need to make changes to a transaction that's already been filed, you can reverse it instead. To do this, create a journal entry with the reverse amounts of debits and credits.

Tip: open the invoice and select More > Transaction journal to view the original debits and credits. Then, enter a journal with the same amount, accounts and VAT (if applicable) on each line. 

Once the journal entry has been created, you can then create a new transaction with the correct information.

For further info, see How to make changes to a transaction that has already been filed in a VAT period on our Community guide. We'll be here if you need any further support.