Fulfillment from multiple locations

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We fulfill orders from our central warehouse but pick stock from a total of three locations (stores).  Shopify is fine for allocating stock from the correct location until we have a situation where the stock is split. For example location one (main warehouse) stocks 2 vases and location two (shop) holds 1 vase.  If a customer orders 3 vases shopify automatically fulfills from location one, pushing the stock there to -1.  The stock in the store will still show as 1 even though it is no longer there.  Obviously the net overall stock figure is still correct but this is causing us a nightmare with trying to keep track of which stock is where!  Is there any way around this?  Many thanks