“Focus” refers to multiple different things in the Glowforge UI, which can be confusing.
There’s the material thickness number, which is used to scale the image taken the by lid camera on your screen so that it’s true to real-world dimensions. Either entering it in “use uncertified material” or using the “set focus” button will both set the material thickness. The camera image will then be re-scaled using this number to more accurately reflect how large things are on your screen vs the real world.
Then there’s the “focus height” for each engrave/cut/score step, which is used to set how high the lens will be raised or lowered in the print head to move the focal point of the laser beam to the desired height. If you enter a number here, that number will be used. If you leave it blank, the placeholder will say “(auto)” and it’ll use whatever material thickness is measured by “set focus” or by autofocus when you hit the print button.
When you put in a material thickness of 0.35", the camera image was scaled on your screen using that information. When you “set focus” and it measured and got a different thickness, it was rescaled with this new information and “shifted” on your screen as a result. Because you put in a focus height of 0.5" somewhere, that would end up being the height the laser beam gets focused at.