Hi,
Problem 1 - now the returns have been submitted I would refrain from trying to make any corrections to them. Make sure to switch the account to the VAT invoicing accounting scheme on the Settings > Details > Tax menu - click on the manage VAT schemes link as per below.
I would advise to create a new scheme to begin from the day after the last submitted return (the day after this quarter ended). When you switch scheme to invoice accounting you will be given two choices of how to deal with the VAT on any unpaid invoices:
You will have to select 'Declare VAT on payment over the next 6 months' as you will have already submitted your last cash accounting return. This means that over the next 6 months the unpaid VAT cash accounting invoices will be added to the return as they are paid. All new invoices will be treated with the invoice VAT scheme and added to returns on their invoice date.
Problem 2 - Once you update the scheme as per above, if you click on any unpaid invoice with an invoice date within this new VAT scheme date range, you can edit the invoice and just click update and the invoice will be treated with the new invoice accounting scheme.
For example if the new VAT scheme is added to begin from the 1st March and you have already added invoices with dates from 1st March onwards, just click on the number hit the edit button and Update at the bottom.
For any invoices that have been paid during this time, you will need to delete the payment first. To do that just click on the invoice number and hit the void button - when prompted just delete the payment.
I hope that all makes sense but if you have any queries just let me know!