When the USGA held the US Senior Open at Saucon Valley, the 13th hole became the 10th so the closing three holes would be the 10th, 11th and 12th. This had to be done because, as I have written in my home course section, you can't place more than 500 people behind the 18th green because there is no room between it and the west patio. I would believe the same will hold true when Saucon hosts the 2009 US Women's Open.
The 1998 US Women's Open at Blackwolf Run used the original 18 holes designed by Dye on the property, but took the original 1st hole (the 37th on the property) plus 9 others on the River and 8 on the Meadows to create the women's open rotation.
I believe the final par 3 at Congressional has been played in different parts of the rotation (see the 1995 US Senior Open rotation compared to the 1997 US Open rotation).
Another point of interest is Southern Hills. In 1977, the 13th played as the par 4 on the back, while 16 played as the par 5. In 2001, the 13th reverted back to the par 5, while the 16th became the par 4.
Lastly, for the USPGA and US Open, it isn't as if people are playing the courses in their normal order because of the two tee starts because golf refuses to tackle the slow play issue. At Bethpage (e.g.), what a start if one has to open on Thursday on the 10th--495, 435 and 515 (now) right out of the gate!