Rotate only a certain part of a frame
Use

 ffmpeg -i IN.MOV
        -filter_complex "[0]split=2[full][crop];
                         [crop]crop=W:H:X:Y,transpose=cclock[crop];
                         [full][crop]overlay='X+h/2-w/2':'Y+w/2-h/2'"   out.mp4


The video is split with one copy getting cropped and rotated. The other full copy remains full-sized. Then the edited portion is overlaid on the full portion.

The variables in capital letters should be replaced with your numerical values.