The Channel ordering in live:cut depends on which Channels were selected for the live:cut project in the first place. For instance, when you have four Channels selected in Just Control, then you will have four Channels in your live:cut project. Channel ordering goes from top left to bottom right, as shown in the following screenshot.
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In case you have four Channels connected in Just Control but you are only using two Channels (in this example, Channel 1 and Channel 4) for live:cut, the Channel ordering will change accordingly. Please refer to the screenshots below (Channel 2 and Channel 4 are connected but not active in live:cut mode).
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If you are working with a different set of channels for different scenes, and you want that CAM 4 always sticks as CH 4 in live:cut, then you can accomplish that with different live:cut templates and Channel mappings. This means that you will have to create a live:cut Template for each scene. So you will end up having a live:cut project for a three-camera scene, a five-camera scene, and so on.