Geoff
I find it more strange that MacKenzie's plan is missing.
I realize that all sorts of plans have been lost through the years--clubhouse fires, floods, the entire course and clubhouse gets washed out to sea or they are just thrown away. Some of these plans aren't all that attractive (for example Egan's) or they were designed for the field. I'm not sure I've ever seen a Thomas plan (other than what's in his book). But whatever the reasons too many are gone.
As far CPC is concerned, I don't believe it was effected by a fire or flood or storm. The club and the Del Monte company appears to have enjoyed many years of stability (relative to other clubs) -- another reason why plans get misplaced or lost.
On the other hand there are quite a few MacKenzie plans that have survived, Ohio State has one, Michigan has one (its actually Maxwell's plan), Valley Club, Augusta National (found their plan not too long ago), Uruguay, Adelaide, Sacramento, St.Charles, Alwoodley, and I'm sure there others I'm not aware of.
One of the reasons I believe his plans survive, is because they are attractive, they are designed for presentation, art if you will. I suspect that many his plans find themselves in a frame early on and once in the frame there chances for survival is good (they aren't rolled up sitting in a corner). There were scores of clubs around the world that had MacKenzie's plan for Old Course hanging on their walls...surely an original would be even more prized. (IMO the green drawing survival is less likely, smaller, easier to loose or throw out, often not framed).
Cypress Point the day it opened was considered a spectacular world class golf course, designed by a world famous architect. And that reputation never waned, the club has always been well aware of their status worldwide...and I'm sure quite proud of it. You would think the club would have preserved much of their records, and it appears they did....numerous letters, the prospectus, the early stick routing, the Albert Barrows rendering. I find it odd the plans are unaccounted for.
I also, for whatever reason, have inclination that Raynor's plan is around somewhere, perhaps in an unlikely spot -- although its survival is more a long shot. If his plans didn't survive, I would think a written description is out there somewhere.