According to this thread in Handbrake forum, I have tried to trim Handbrake encoded .m4v file without re-encode whole video.
It worked nicely.
- Download MPEG Streamclip from this site.
- Open .mp4 file with MPEG Streamclip.
- Set in-point and out-point, then trim it.
- Save file in another .mp4 file.
- Change extention to .m4v
iPad default video player could play it without problem.