Unfortunately the MWS API (the system Amazon allows 3rd parties to communicate with them through) has not been updated to handle combining commingled inventory with seller labeled inventory. That being said, there is a workaround in InventoryLab, if you want to send all of your products within one shipment.
You will want to choose the option to “Send Product Feeds” at the end of your shipment and use those product listings to create shipment plans from the items you listed from InventoryLab.
This is basically bypassing the “create shipment” step in InventoryLab and using Seller Central to create your shipments. In order to do this, click “Send Products” on the List & Prep page, and then “Submit” on the next page like you normally would. However, when you get to the final popup box, you’ll want to uncheck the box for “create FBA shipment” so that the send product feeds is the only box checked, and then click Sync so that the batch becomes “Closed.”
From Inventory>Closed Batches you'll choose to Export and a drop down will give you two options. Click Shipping plan to download the batch information into a .txt file which contains all of the data within the batch needed for the FBA shipping plan.
As outlined Here.
Note: You must wait 15 to 30 minutes for your feeds to fully send your listings over to Amazon prior to uploading your Inbound Shipping Plan into Seller Central. If you attempt the upload too early, Amazon will give an “Unknown SKU. The SKU for this product is unknown or cannot be found.” error.