For some strange reason, when I rotate a PDF using the trackpad (Two finger multi-touch rotation gesture.), there's no option to save it and all changes are lost after I close it.
(The save button is grayed out.)
What am I doing wrong?
... Never mind. Apparently rotating using the trackpad of a PDF in Preview is just for cosmetic purposes. You have to rotate using +L or +R or within the Apple-bar menu. Only after that, the save option will be available. :|
Like you said, using + L and +R seems to modify the PDF in place.
But if you use the rotation gesture on the trackpad, and use
Save As, it will save the PDF with the pages rotated.