I spent about 5 hours Friday breaking everything down, cleaning, and then refilling the pond. All the fish survived, although it got a little dicey near the end. Even though I had good aeration, the fish are larger than last year, and were really using up the oxygen in the temporary pond. One was on the brink, and I had to toss him into the turtle pond. Temperature change was great, but he was just happy to have oxygen.
They were doing pretty poorly, and so I had to start putting them into the pond even before it was completly filled. There was a big temperature difference, about 10*, but the first ones I put in did OK. Then I rembered Marla's point about mixing the pond water with the water in their temporary tank, and that helped equalize the temperatures more quickly.
I did NOT find any turtle, so am still at a loss to know what caused the wound on my koi.
There was a lot more gunk on the bottom than I had thought, so I'm glad I cleaned it all out. Also, my old water was clear, but it was stained by leaves and such. Now with the fresh new water, you can see all the way to the bottom of the 36" deep section.