Hey, I just want to modify the layer and the sorting layer after I make the map on tiled but there is no applying like original prefab after changing the layer or sorting layer .
This isn’t a Tiled issue. Tiled can’t change the behaviour of Unity.
You will need to modify the original TMX (TSX is tilesets, I assume you meant TMX, a map?) in Tiled and re-import it into Unity to update it. I haven’t used SuperTiled2Unity myself, but presumably it has some way to just update the prefab without making a new one, so that all scenes using it will be updates.
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Actually, I already re-import and update thing in tiled but just same, I figure it out just make it to prefab variant or new prefab so can update the layer and sorting layer, it’s kinda slow because 2 times work 
for me.