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Two shapes used the same pattern/sprite set with different color palettes to hide/show different part of the sprite  by switching a color index to black - the background one :)

Oh, I see! Is there a way to correct this, or is it just stuck like this? I'm unsure how, or even if this could be solved, really.

Create two instances for that pattern. And in script enable one, disable one based on the shape color palette.