Ship with FBA is designed to work with multi-item orders on Shopify. Each line item in the order is attempted to be fulfilled via FBA. In case one or more SKUs is not fulfillable (due invalid SKU, insufficient inventory, etc) then you can configure the app to either of the following options:
1. Fulfill partial order
If this option is selected, the app will partially fulfill the order by shipping the items having valid SKUs. Invalid SKUs will be skipped.
2. Do not fulfill the order
In this case, the order will not be shipped at all, if it contains one or more invalid items. Only if all the line item SKUs of the order are valid, then the order will be shipped via FBA.