What you need to do is open both Cmd.cfg files in NotePad and compare them side-by-side. This way you can see exactly what gets changed from one mod to the next. Then you can make a third one combining the two to get exactly what you need.
You may find that both are the same. JSGME warns you that one is about to overwrite the other. It doesn't actually read the document to know exactly what was changed. If they're identical then you can just click "Sure, go ahead and overwrite the thing. I don't care!"
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“Never do anything you can't take back.”
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