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 can be seen shown in the following screenshot.
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In case you have four channels connected in Just Control and but you are only using two channels (in this caseexample, Channel1 Channel 1 and Channel4Channel 4) for live:cut, then the channel ordering changes will change accordingly. Please see the screenshots below (Channel2 Channel 2 and Channel4 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 CAM4 CAM 4 always stays sticks as CH4 CH 4 in live:cut, then you can do accomplish that with different live:cut templates and channel mappings. That This means that you will have to create a live:cut template Template for each scene. So you will have end up having a live:cut project for a three-camera scene, a five-camera scene, and so on.