Give an .i3d model a new texture: see how its UVs lie, paint over them, and save it back.
Open File, pick Open, and choose the .i3d file along with its texture images, the PNGs its materials name. They show on the model at once, on the File preview with Textures on in the 3D View. A material with "!" in its name shows its key color clear: see Opacity maps and color keys.


Paint the new texture over the SVG in an image editor, at the old texture's size: see Paint a texture over the SVG layout. For a material with "!" in its name, the first color of a paletted PNG shows clear, or pure black in one without a palette: paint what's to be cut out in that color.
The saved model still names its old texture file, so save the new PNG under that same name, beside the model.