There are various channel specific settings depending on the channels you are using in StoreAutomator.
This switch is located on the Channel>Channel Settings>Amazon Settings tab.
When this switch is enabled, SA ignores the FBA existence on your inventory, and sends the products as FBA to Amazon. You can use this if you want to ignore FBA's existence and convert your products to FBA on the channel.
IMPORTANT NOTE: Switching on this settings will apply to all products and your items will be switched to FBA if they have FBA labels in the selected Amazon channel.