There are two files: Unit_HUD_InfoCard and Unit_HUD_Main. These two affect all instances of the icon you're referring to (on the star map, in the galaxy window, and in the info card fleet summary).
Be sure you change both the color channels and the alpha channel, and then make certain you place the new icon into the EXACT same place on the canvas. The brush files dictate which parts of the canvas are used for which ship, and if you go outside the boundaries of the Radiance quadrant you won't get your entire icon (plus part of your new icon will become part of another ship's icon).
