Looks good. Even more zenful now without the page refreshing. I'm curious about how you cut the polygons. Is that a builtin feature for the polygons in Godot? I use Godot but haven't done much in that vein.
Viewing post in Chuang Tzu: The way of the Butcher (Director's cut) comments
There is a helper class called Geometry2D which contains many functions that interact with polygons and lines. I highly recommend to watch this video that describes them. After you draw a curve the game creates a polygon that starts from the bottom and ends with that curve, then an intersection is calculated.
The problem with the disappearing polygons is that after the clipping is done the vertices order sometimes gets messed up - the polygon is still there, but because the points are not ordered sequentially, some parts get inverted and then the whole thing becomes invisible.