Prevent duplicate eBay orders from importing through Shopify

Shipstation already has a store setting for Volusion stores that prevents eBay orders from importing through Volusion. We need the same for Shopify. We sell on Shopify and on eBay. I have both sales channels added to Shipstation. Recently, Shopify has added an eBay integration. We have mapped a few products so their inventories are shared, and the items can be sold on both marketplaces with shared inventory. Shipstation now brings in two orders for ever order placed for these mapped items, one from Shopify and one from eBay. We're hand managing each order for now, but this invites errors. I fear some orders will be shipped twice. Please help!