When I use:

JS.setCss (".ui-icon", "display:none")

If you just delete a line of code from the init script does quest core code return to original when saved or reloaded?
Should I replace it with correct code then delete it?
Does this permanently change Quest?
Who am I?
Where's Waldo?

When you use the JS code, it changes the CSS rules for the lifetime of the browser session (as long as the game is actively being played; so it reverts when the game is closed and reloaded)

If you put that code in the UI initialisation script, it applies the change when a new game is started, and when a saved game is loaded. That's necessary because the state of the browser isn't included in the saved game.

It doesn't permanently change anything. It only changes a variable which is stored in-memory, and is not saved with the rest of the game.