Spark Shipping does not remove products from your store.
With inventory automation, when a vendor sets a quantity of 0 Spark Shipping will mark that product as a 0 quantity.
Your shopping cart then controls what happens next. From there you can set your shopping cart to show the item as out of stock, remove the product from your site, etc.
Also see - How to automatically mark a product as out of stock when the vendor no longer carries this item
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