Texture Studio

Open folder… and click a picture. Select what to change — Magic wand / Colour range (click a colour), Lasso, Rectangle; Shift adds, Alt takes away — then Recolour it and Apply.

Save .dds writes the game's format (DXT1 / DXT5 with mip maps, like its own textures); Convert folder to .dds… does every .png of the folder at once. Wheel: zoom, middle / right drag or Space: move.