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You can create as many layer states as you need. If you have two viewports in your layout, you can create a layer state for each one to display different layers in each viewport. But, if you go into model space and start freezing layers, as tombu mentioned, that will affect your viewport display when you go back to your layout and those layers that you froze in model space will no longer be visible in your viewports. I believe this is the problem you are describing. Once you create your layer states, it's best to leave model space alone. Just work inside your viewports.