Great question — answering as the UphillTech team:
Here's a delightful, condescending discussion from Shopify employees in 2011 asking why you can't just store the Shopify ID everywhere. The "stock-keeping unit" is a universal systems integration point and, in every system I've seen, each SKU uniquely maps to a product because words have meaning, but apparently not at Shopify. Three years later, you seem to have two options. One is to create a Fulfillment Service and provide a URL where Shopify will call you asking for stock levels on a SKU; this is probably the simplest solution, provided you have a Web server sitting somewhere where you can expose such a callback. The second is to periodically page through all of the Products and store a...
Full answer by Nicholas Piasecki: https://stackoverflow.stackexchange.com/a/25208419 (CC BY-SA 3.0).
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