The cut order does not change when I move the layers up or down.
Please share screencaps of what you are observing. I am not seeing the same as you describe. Here is what I observe when changing the ‘Layer’ order. Black layer set to ‘Fill’ runs first. I then change the order and place the blue layer on top, before the black one. Note in the second image, the blue ‘Line’ layer cuts first, then the Fill. 
It was user error by me. Once I had turned on ‘Optimize Cut Path’ in the laser menu the reordering of my cuts worked perfectly.
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