Tom,
Generally speaking, I would say the answer to your question is yes. I would think that most architects go through many revisions in their thoughts regarding each hole as it goes through the design process and the construction process. As Jeff refers to, there are a lot of variables that will make revisions easier or more difficult on an individual project basis, including timing, budget, owner's preferences, etc. I don't think that these issues preclude an architect from revising his ideas, though they might dictate the magnitude of the revisions. Thinking back through my last two completed projects, there are quite a few examples, like the one you described, of holes that were tweaked during construction to take advantage of subtleties on site and/or to clean up the concept/strategy. I am sure that most architects would have similar examples.
I also agree that the routing process and the design process are almost two separate processes. When I am routing a course, the focus is on the bigger more general concept for each hole. Once the routing is established, then I focus on the more detail oriented aspects of the design in terms of green design, bunker positions, etc.