We'll see how 20+ year old files stand up to a modern HD treatment when it happens. For right now, I'd assume that it would be easier and more practical to just recreate new ships from scratch with the newest CG technology.
Have you even read the article on TrekCore? It says that the models were generally "overbuilt" for SD resolution by the CGI artists.
With some tweaks and obviously some updated/higher res versions of the ship's textures it sure seems like they could be just fine. Re-rendering them with modern tools to create more realistic interactive lighting, etc. would make all the difference. That is not starting over from scratch, just enhancing what assets they have. As FrontierTrek said, it would be one helluva task to actually start from scratch.