It sounds like you need to hide the specific sublayer. In that case, you need to get the sublayer instance and set its listMode to hide. Here's a sample app that does this. If you comment out the following code, you will see the sublayer appear in the LayerList. Leave it, and it is removed, but remains in the map.
LayerList widget - 4.7
var walkCurrentLayer = view.map.layers.flatten(function(item){
return item.layers || item.sublayers;
}).find(function(layer){
return layer.title === "walkability current";
});
walkCurrentLayer.listMode = "hide";