So this question has an incorrect title as You already did set up a multistore. Instead of this You should be asking How to disable a product on just one store within a multistore installation?
, shouldn't You?
The problem is clear and the answer too - You cannot do this by enabling/disabling the product/category, etc. The multistore
feature allows You to have only one database while You can set a product (or category or whatever) to show on store 1 to store X.
If You disable the product, You disable it for all stores.
If You want a product to be shown only at store 2 but not at store 1, check/uncheck the appropriate checkboxes within a product detail form at tab Links -> option Stores. By unchecking Default
and checking e.g. Store 2
You set the product to be shown only at store 2 - but the product has to be enabled. Same way for categories, manufacturers, etc.
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