Sanding through epoxy will generally cause a color change at least at the edge of the partially sanded area. The best bet is to sand everything equally to make it uniform.

Actually precoating the boat before adding veneer is a good idea because it can help avoid this problem in reverse. If you epoxy down the veneer and any epoxy finds its way away from the inlay, it can cause a halo around its perimeter. By coating the whole boat there is no perimeter. Just don't sand the epoxy before applying the veneer. You can sand lightly, you just don't want to sand through.