Yes, but I have a LOT of h.264 in MKV, so its a major conversion job that I'm trying to avoid![]()
I've just finished remuxing about 4.5 terrabytes of anime for playing on my new ATV 3. It took me about a week to do on my "old" i3 iMac with handbrake. Remuxing isn't as long as doing a full recompress. You can use Subler for that. In my case I had to burn in the subtitle track so I used Handbrake which does offer batch processing. While setting the different parametters and selecting the audio and subs track was a pain, it took only a couple of hour and then at the press of a button the job was launched and executed in the background.
Most of my remaining 12 terrabytes of movies and TV episodes are already in m4v/mp4 (dvd rip or captured with Osprey/HD PVR/EyeTV HD), but I still have a bunch of them in old AVI/Mpeg2 or MKV to process.