Using ffmpeg on MOV files created by iMovie It looks like ffmpeg will not work with MOV files created using iMovie. Is there a way to batch convert these files (which are HUGE) to a compressed format, preferably mp4? I've also tried HandBrake with no success (though I assume ffmpeg is under the hood).
You may try MPEG StreamClip also. There is Batch mode — cmd+b

But it's hard to tell based on your information why Handbrake was not able to help you.