Wade:
From anecdotal experience, this happens much more often than you would think.
Partly, it's just one of those topics where every client has an opinion, and there's a reasonable chance their opinion will differ from the architect's. The Tour has done it quite often, too, for logistics reasons or something or other.
I can remember discussing it for my own courses on six or seven different occasions [which is a lot, considering I've built a fair number of courses that don't return at #9]. It almost seems that if you don't design to the cliche of a fairly wide open first hole and a harder tenth hole and a crescendo finish, you are inviting someone to suggest turning it around.
That said, at least half of the courses I know of that switched nines after the course had been open for years, wound up switching them BACK later on. Part of that is just familiarity -- you hate it when what you've always referred to as the 2nd hole at Somerset Hills is now the 11th. But the rest is an admission that maybe the original architect had reasons for his choice.