This message usually populates when information for a "Working" shipment in Stratify no longer matches up with your Seller Central Shipping Queue. For example, there could be a shipment showing in the Working Shipments area of your List>List & Prep page that has been marked as "Shipped" or deleted.
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Solution:
To clear this message, try clicking the Sync Shipments button next to Working Shipments before adding the item to your batch once more.
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If the error still populates at that point, you may also have to log out of Stratify and then back in for this to clear.