On the flat rate scheme, the only transactions that should appear on a VAT return are sales, or purchases above £2000 if it is classed as a fixed asset.
If you have entered sales bank transactions but these are not appearing on the VAT return, the result for this could be due to the way the nominal code used as been set up.
To ensure that all sales bank transactions appear on the VAT Return you will need to go to Settings> Chart of Accounts and ensure that the type is set to “Turnover”. If the code has been set to “Expenditure” or “Cost of sale” then this will not appear on the VAT Return if you are on the Flat Rate Scheme.
You can read more information on this by clicking on this link.