You can certainly do this between an inventory system and Shopify. You could simply set your Shopify item to not be available which is a simple option.
Or, using an inventory system like SKUSavvy you can connect your Shopify store and hold inventory there, then make the product unavailable at a certain inventory level. In your scenario, you could make 10 available to your Shopify channel, which would then update your Shopify to show out of stock until you relist the items, while still holding 490 items in the inventory around your warehouse bins.
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