Uploading Tracking via FTP for MDC Orders

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We're operating multiple warehouses across the country and sometime fulfilling multiple line orders from multiple warehouses. I know that there's a way to create multiple shipments to an order via the ChannelAdvisor web app (screenshot) but how can we add another tracking number to an order when uploading tracking numbers via FTP? We're following the process described in the Creating a File for Bulk Upload of Shipping and Tracking Information but there's no way to assign the shipment to an item, only to the entire order (see The Import Shipping and Tracking File Template). And if the order already has one shipment, ChannelAdvisor returns an error instead of accepting the tracking numbers. This issue is causing marketplaces to refund orders that we shipped, losing a lot of money, and a high pre-fulfillment cancellation rate. We're currently in a risk of losing our Jet account.



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-Ben Sharir