One of the problems I’ve had using Apple’s (now end-of-lifed) Aperture photography software, is that it doesn’t make changes to an original RAW file. Everything changed within it is done using versions – essentially metadata – so that you can have a dozen different variants of a file, but only ever have one taking up space on disk.
It’s a great idea, except when your original has a problem, like for example the camera has recorded orientation information that you don’t want applied. Aperture provides no way to alter the RAW file. You can create a rotated version in Aperture, but exporting the RAW will output the original un-rotated edition.
The solution is to use Nikon’s own ViewNX software. It’s ugly as sin, not at all Mac-like, but when you rotate a RAW file in it, the file on disk is rotated, while staying as a RAW.
Then, you have to reimport the image as a new file, and delete the old version. Simply replacing the old one with the rotated version in Aperture’s library won’t show up as having been changed when you re-launch Aperture.