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Will this work on iPads or Apple TVs?

It depends on the nature of the h.264 tracks in the mkv files. I use MakeMKV to rip my BluRays directly to high bitrate 1080p MKV files. Then I use Handbrake to recode them down to the AppleTV2 preset. While my WDTV Live box can handle the BluRay rips, my AppleTV certainly can't.

If yor MKV's are downloaded 720P files, the h.264 streams may well be compatible with the AppleTV 2. I'd give it a try and see how it goes.
 
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Don't use handbrake to transcode mkv to mp4!

Simply use mkvtools to passthru the 264 or mpeg4 tracks!

It is quite rare for the mkv to have an H264 format video that will playback on ATV (1 or 2) they tend to be H264 with extra profile options enabled meaning they playback fine on your Mac but the ATV or iPad will reject when you try and play.

Edwin
 
It is quite rare for the mkv to have an H264 format video that will playback on ATV (1 or 2) they tend to be H264 with extra profile options enabled meaning they playback fine on your Mac but the ATV or iPad will reject when you try and play.

Edwin

That may be true for ATV1 but it's certainly not true for ATV2. If they are encoded with sane H.264 options they'll play fine on the ATV2 and all recent iOS devices.
 
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