Many people have Custom Transaction Numbers enabled in QuickBooks Online without realizing it. With Custom Transaction Numbers enabled, QuickBooks Online will not provide Invoice numbers when you create an Invoice through Breadwinner (or any other QuickBooks Online Integration).
If you have Custom Transaction Numbers enabled, when you create your Invoice using Breadwinner you will have the option to provide an Invoice Number just before Invoice creation. Please be aware that QuickBooks Online will reject duplicate numbers but will accept blank numbers.
Additionally, if you want to populate this Custom Transaction Number / Invoice Number from a custom field on your Opportunity, you may do so at the Breadwinner Professional edition and up.
To Populate the Custom Transaction Number from an Opportunity Custom Field (which requires Breadwinner Professional and up) please specify which custom field you want in the Breadwinner tab, in the Invoice Configuration section.
Alternatively, if you wish do Disable Custom Transaction Numbers, then in QuickBooks Online, click the gear and follow the screenshots.
Click Company Settings
Click Sales, then click the Pencil
Uncheck the Custom Transaction Number setting and Save