There are plenty of examples of what they call "total blow ups" where a new course is built over an old one of low merit. I did a remodel on a course near Kilgore a few years back. When I first stepped on the site, my reaction was that the existing course was the worst course I had seen, on the best piece of property. (They decided the local pro and an engineer were all they needed to lay it out.) So, it happens.
Generally, it's hard to find a course where the original gca missed.....absolutely.....every.......good hole. But, there are some. I won't mention names, but one of the lesser lights of the Chicago School had hit on a design method (I think on plans, where those control points were easy to see because of lack of contour lines) of locating all tees, greens, and landing zones on hilltops, which wasn't great for the 99% who miss those ideal landing zones some or most of the time. I was asked to renovate one of his courses, and my comment was that he had "missed every natural golf hole out there by at least a few yards." So, that is a case of a professional architect who somehow built a course mostly lacking in merit. (Although I think it is still out there)
And at least one signature architect has had 2 or 3 of his courses remodeled before they even opened, although I'm not sure exactly why, so big name architects aren't totally immune.