I have a couple of hours of 253 images shot east and a couple of hours shot west after a flip. What I've done is stack the easterly shots and then the westerly shots, saved the results as 16bit tif files, rotated one and stacked those 2.
Is there another way to do this without reducing them to 16bit. Is there a tool to rotate canon raw files or even 32bit tif files?
in direct answer to your question though, Photoshop will rotate 32bit tiff's with no probs at all.. Remember, your 40D does not have a 32bit depth, it has a 16bit depth.. so saving the images as 16bit does not do them any damage at all.