Automated collections with no conditions

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I recently volunteered and built a Shopify site for a local retailer. Her inventory system is pushing everything over to Shopify correctly, but her 4 main categories are automatically creating collections that aren't editable. By that, I mean I can't set conditions on this 4 collections. I've created a greater than 0 condition on sub-collections that works, but the products that have zero inventory still show under the main collections. Any suggestions on how to handle this or am I going to have to find an app that will monitor her inventory real-time and hide these products in the main collections when they are sold out? Appreciate the assistance up-front and I hope everyone is staying safe.