Fix (unreported) missing updates in scripts/docs after scene.update() removal.

This should really have been done together with API changes, simple
usage of grep does the trick to catch most places needing updates.

tests/python/view_layer/test_evaluation_visibility_e.py

@@ -40,7 +40,7 @@ class UnitTesting(ViewLayerTesting):
         layer_collection_mom.enabled = True
         layer_collection_kid.enabled = False
 
-        bpy.context.scene.update()  # update depsgraph
+        layer.update()  # update depsgraph
         self.assertTrue(cube.visible_get(), "Object should be visible")