Yes, you can change the atlas. I’m guessing you are using sprite components? In that case the property is called “image”, and you can swap it out using go.set:
go.set("#sprite", "image", some_atlas_path)
You can use script properties to define a bunch of atlases you want to switch between as well:
-- these need to be specified at the top of your script:
go.property("skin_base", resource.atlas())
go.property("skin_xmas", resource.atlas())
function init(self)
-- it's christmas!
go.set("/go#sprite", "image", self.skin_xmas)
end